How to Model Inter- and Intramolecular Hydrogen Bond Strengths with Quantum Chemistry.

Abstract:

:This article presents the computation of both inter- and intramolecular hydrogen bond strengths from first-principles. Quantum chemical calculations conducted at the dispersion-corrected density functional theory level including free energy and solvation contributions are conducted for (i) one-to-one hydrogen-bonded complexes of alcohols to N-methyl pyrrolidinone measured by an infrared spectroscopy method and (ii) a set of experimental intramolecular hydrogen bond-forming phenol and pyrrole compounds, with intramolecular hydrogen bond strengths derived from a nuclear magnetic resonance method. The computed complexation free energies in solution show a correlation to experiment of R2 = 0.74 with a root mean square error of 4.85 kJ mol-1. The intramolecular hydrogen bonding free energies in solution show a correlation of R2 = 0.79 with a root mean square error of 5.51 kJ mol-1. The results of this study can be used as a guide on how to build reliable quantum chemical databases for computed hydrogen bonding strengths.

journal_name

J Chem Inf Model

authors

Bauer CA

doi

10.1021/acs.jcim.9b00132

subject

Has Abstract

pub_date

2019-09-23 00:00:00

pages

3735-3743

issue

9

eissn

1549-9596

issn

1549-960X

journal_volume

59

pub_type

杂志文章
  • Flux (1): a virtual synthesis scheme for fragment-based de novo design.

    abstract::It is demonstrated that the fragmentation of druglike molecules by applying simplistic pseudo-retrosynthesis results in a stock of chemically meaningful building blocks for de novo molecule generation. A stochastic search algorithm in conjunction with ligand-based similarity scoring (Flux: fragment-based ligand builde...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci0503560

    authors: Fechner U,Schneider G

    更新日期:2006-03-01 00:00:00

  • Expert system for predicting reaction conditions: the Michael reaction case.

    abstract::A generic chemical transformation may often be achieved under various synthetic conditions. However, for any specific reagents, only one or a few among the reported synthetic protocols may be successful. For example, Michael β-addition reactions may proceed under different choices of solvent (e.g., hydrophobic, aproti...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci500698a

    authors: Marcou G,Aires de Sousa J,Latino DA,de Luca A,Horvath D,Rietsch V,Varnek A

    更新日期:2015-02-23 00:00:00

  • Computational and conformational evaluation of FTase alternative substrates: insight into a novel enzyme binding pocket.

    abstract::Protein farnesyltransferase (FTase) is an important anticancer drug target. In an effort to develop isoprenoid diphosphate-based FTase inhibitors, striking variations have been observed in the ability of conservatively modified analogues to bind to the enzyme. For example, 2Z-GGPP is an alternative substrate with high...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci0496550

    authors: Henriksen BS,Zahn TJ,Evanseck JD,Firestine SM,Gibbs RA

    更新日期:2005-07-01 00:00:00

  • Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank.

    abstract::Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-ray crystallography takes into account XBs, which might result in the weakening or even vanishin...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.7b00235

    authors: Zhang Q,Xu Z,Shi J,Zhu W

    更新日期:2017-07-24 00:00:00

  • Loop Grafting between Similar Local Environments for Fc-Silent Antibodies.

    abstract::Reduction of the affinity of the fragment crystallizable (Fc) region with immune receptors by substitution of one or a few amino acids, known as Fc-silencing, is an established approach to reduce the immune effector functions of monoclonal antibody therapeutics. This approach to Fc-silencing, however, is problematic a...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b01198

    authors: Lešnik S,Hodošček M,Podobnik B,Konc J

    更新日期:2020-11-23 00:00:00

  • Comments on the article "Evaluation of pK(a) estimation methods on 211 druglike compounds".

    abstract::The recent article "Evaluation of pK(a) Estimation Methods on 211 Druglike Compounds" ( Manchester, J.; et al. J. Chem Inf. Model. 2010, 50, 565-571 ) reports poor results for the program Epik. Here, we highlight likely sources for the poor performance and describe work done to improve the performance. Running Epik in...

    journal_title:Journal of chemical information and modeling

    pub_type: 评论,杂志文章

    doi:10.1021/ci100332m

    authors: Shelley JC,Calkins D,Sullivan AP

    更新日期:2011-01-24 00:00:00

  • Predicting the DNA Conductance Using a Deep Feedforward Neural Network Model.

    abstract::Double-stranded DNA (dsDNA) has been established as an efficient medium for charge migration, bringing it to the forefront of the field of molecular electronics and biological research. The charge migration rate is controlled by the electronic couplings between the two nucleobases of DNA/RNA. These electronic coupling...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c01072

    authors: Aggarwal A,Vinayak V,Bag S,Bhattacharyya C,Waghmare UV,Maiti PK

    更新日期:2021-01-25 00:00:00

  • Ligand- and structure-based virtual screening for clathrodin-derived human voltage-gated sodium channel modulators.

    abstract::Voltage-gated sodium channels (VGSC) are attractive targets for drug discovery because of the broad therapeutic potential of their modulators. On the basis of the structure of marine alkaloid clathrodin, we have recently discovered novel subtype-selective VGSC modulators I and II that were used as starting points for ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci400505e

    authors: Tomašić T,Hartzoulakis B,Zidar N,Chan F,Kirby RW,Madge DJ,Peigneur S,Tytgat J,Kikelj D

    更新日期:2013-12-23 00:00:00

  • Generalized topological indices. Modeling gas-phase rate coefficients of atmospheric relevance.

    abstract::We develop the idea that the use of ad hoc molecular descriptors in QSAR/QSPR studies is not an optimal solution. Instead, we propose to optimize these descriptors for the specific properties under study. In the case of topological indices (TIs) we propose the use of the generalized topological indices (GTIs), which a...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci600448b

    authors: Estrada E,Matamala AR

    更新日期:2007-05-01 00:00:00

  • Symplectic molecular dynamics simulations on specially designed parallel computers.

    abstract::We have developed a computer program for molecular dynamics (MD) simulation that implements the Split Integration Symplectic Method (SISM) and is designed to run on specialized parallel computers. The MD integration is performed by the SISM, which analytically treats high-frequency vibrational motion and thus enables ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci050216q

    authors: Borstnik U,Janezic D

    更新日期:2005-11-01 00:00:00

  • Computational simulations of the interactions between acetyl-coenzyme-A carboxylase and clodinafop: resistance mechanism due to active and nonactive site mutations.

    abstract::Grass weed populations resistant to acetyl-CoA carboxylase-inhibiting (ACCase; EC 6.4.1.2) herbicides represent a major problem for the sustainable development of modern agriculture. In the present study, extensive computational simulations, including homology modeling, molecular dynamics (MD) simulations, and molecul...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci900174d

    authors: Zhu XL,Ge-Fei H,Zhan CG,Yang GF

    更新日期:2009-08-01 00:00:00

  • Substituted 4,5'-Bithiazoles as Catalytic Inhibitors of Human DNA Topoisomerase IIα.

    abstract::Human type II topoisomerases, molecular motors that alter the DNA topology, are a major target of modern chemotherapy. Groups of catalytic inhibitors represent a new approach to overcome the known limitations of topoisomerase II poisons such as cardiotoxicity and induction of secondary tumors. Here, we present a class...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.0c00202

    authors: Bergant Loboda K,Janežič M,Štampar M,Žegura B,Filipič M,Perdih A

    更新日期:2020-07-27 00:00:00

  • Phosphorylation of Fibronectin Influences the Structural Stability of the Predicted Interchain Domain.

    abstract::As a key player in cell adhesion, the glycoprotein fibronectin is involved in the complex mechanobiology of the extracellular matrix. Although the function of many modules in the fibronectin molecule has already been understood, the structure and biological relevance of the C-terminal cross-linked region (CTXL) still ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.9b00555

    authors: Kulke M,Uhrhan M,Geist N,Brüggemann D,Ohler B,Langel W,Köppen S

    更新日期:2019-10-28 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

  • Effects of Ligand Environment in Zr(IV) Assisted Peptide Hydrolysis.

    abstract::In this DFT study, activities of 11 different N2O4, N2O3, and NO2 core containing Zr(IV) complexes, 4,13-diaza-18-crown-6 (I'N2O4), 1,4,10-trioxa-7,13-diazacyclopentadecane (I'N2O3), and 2-(2-methoxy)ethanol (I'NO2), respectively, and their analogues in peptide hydrolysis have been investigated. Based on the experimen...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.6b00781

    authors: Zhang T,Sharma G,Paul TJ,Hoffmann Z,Prabhakar R

    更新日期:2017-05-22 00:00:00

  • Multiple e-pharmacophore modeling, 3D-QSAR, and high-throughput virtual screening of hepatitis C virus NS5B polymerase inhibitors.

    abstract::The hepatitis C virus (HCV) NS5B RNA-dependent RNA polymerase (RdRP) is a crucial and unique component of the HCV RNA replication machinery and a validated target for drug discovery. Multiple crystal structures of NS5B inhibitor complexes have facilitated the identification of novel compound scaffolds through in silic...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci400644r

    authors: Therese PJ,Manvar D,Kondepudi S,Battu MB,Sriram D,Basu A,Yogeeswari P,Kaushik-Basu N

    更新日期:2014-02-24 00:00:00

  • Molecular Mechanism, Dynamics, and Energetics of Protein-Mediated Dinucleotide Flipping in a Mismatched DNA: A Computational Study of the RAD4-DNA Complex.

    abstract::DNA damage alters genetic information and adversely affects gene expression pathways leading to various complex genetic disorders and cancers. DNA repair proteins recognize and rectify DNA damage and mismatches with high fidelity. A critical molecular event that occurs during most protein-mediated DNA repair processes...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.7b00636

    authors: Pitta K,Krishnan M

    更新日期:2018-03-26 00:00:00

  • Long-range effects of a peripheral mutation on the enzymatic activity of cytochrome P450 1A2.

    abstract::The human cytochrome P450 1A2 is an important drug metabolizing and procarcinogen activating enzyme. An experimental study found that a peripheral mutation, F186L, at ∼26 Å away from the enzyme's active site, caused a significant reduction in the enzymatic activity of 1A2 deethylation reactions. In this paper, we expl...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci200112b

    authors: Zhang T,Liu LA,Lewis DF,Wei DQ

    更新日期:2011-06-27 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

  • Tyrosine Regulates β-Sheet Structure Formation in Amyloid-β42: A New Clustering Algorithm for Disordered Proteins.

    abstract::Our recent studies show that the single Tyr residue in the sequence of amyloid-β42 (Aβ42) is reactive toward various ligands, including metals and adenosine trisphospate (see: Coskuner , O. J. Biol. Inorg. Chem. 2016 , 21 , 957 - 973 and Coskuner , O. ; Murray , I. V. J. J. Alzheimer's Dis. 2014 , 41 , 561 - 574 ). Ho...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.6b00761

    authors: Coskuner O,Uversky VN

    更新日期:2017-06-26 00:00:00

  • Virtual Screening with Generative Topographic Maps: How Many Maps Are Required?

    abstract::Universal generative topographic maps (GTMs) provide two-dimensional representations of chemical space selected for their "polypharmacological competence", that is, the ability to simultaneously represent meaningful activity and property landscapes, associated with many distinct targets and properties. Several such GT...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.8b00650

    authors: Casciuc I,Zabolotna Y,Horvath D,Marcou G,Bajorath J,Varnek A

    更新日期:2019-01-28 00:00:00

  • Accurate prediction of adsorption energies on graphene, using a dispersion-corrected semiempirical method including solvation.

    abstract::The accurate prediction of the adsorption energies of unsaturated molecules on graphene in the presence of water is essential for the design of molecules that can modify its properties and that can aid its processability. We here show that a semiempirical MO method corrected for dispersive interactions (PM6-DH2) can p...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci5003729

    authors: Vincent MA,Hillier IH

    更新日期:2014-08-25 00:00:00

  • Large-scale mining for similar protein binding pockets: with RAPMAD retrieval on the fly becomes real.

    abstract::Determination of structural similarities between protein binding pockets is an important challenge in in silico drug design. It can help to understand selectivity considerations, predict unexpected ligand cross-reactivity, and support the putative annotation of function to orphan proteins. To this end, Cavbase was dev...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci5005898

    authors: Krotzky T,Grunwald C,Egerland U,Klebe G

    更新日期:2015-01-26 00:00:00

  • Predictive models for cytochrome p450 isozymes based on quantitative high throughput screening data.

    abstract::The human cytochrome P450 (CYP450) isozymes are the most important enzymes in the body to metabolize many endogenous and exogenous substances including environmental toxins and therapeutic drugs. Any unnecessary interactions between a small molecule and CYP450 isozymes may raise a potential to disarm the integrity of ...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci200311w

    authors: Sun H,Veith H,Xia M,Austin CP,Huang R

    更新日期:2011-10-24 00:00:00

  • Consensus QSAR models: do the benefits outweigh the complexity?

    abstract::This study has assessed the use of consensus regression, as compared to single multiple linear regression, models for the development of quantitative structure-activity relationships (QSARs). To provide a comparison, four data sets of varying size and complexity were analyzed: silastic membrane flux, toxicity of pheno...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci700016d

    authors: Hewitt M,Cronin MT,Madden JC,Rowe PH,Johnson C,Obi A,Enoch SJ

    更新日期:2007-07-01 00:00:00

  • Assessing different classification methods for virtual screening.

    abstract::How well do different classification methods perform in selecting the ligands of a protein target out of large compound collections not used to train the model? Support vector machines, random forest, artificial neural networks, k-nearest-neighbor classification with genetic-algorithm-optimized feature selection, tren...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci050519k

    authors: Plewczynski D,Spieser SA,Koch U

    更新日期:2006-05-01 00:00:00

  • Combining 3-D quantitative structure-activity relationship with ligand based and structure based alignment procedures for in silico screening of new hepatitis C virus NS5B polymerase inhibitors.

    abstract::The viral NS5B RNA-dependent RNA-polymerase (RdRp) is one of the best-studied and promising targets for the development of novel therapeutics against hepatitis C virus (HCV). Allosteric inhibition of this enzyme has emerged as a viable strategy toward blocking replication of viral RNA in cell based systems. Herein, we...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci9004749

    authors: Musmuca I,Caroli A,Mai A,Kaushik-Basu N,Arora P,Ragno R

    更新日期:2010-04-26 00:00:00

  • Kinetic Models of Cyclosporin A in Polar and Apolar Environments Reveal Multiple Congruent Conformational States.

    abstract::The membrane permeability of cyclic peptides and peptidomimetics, which are generally larger and more complex than typical drug molecules, is likely strongly influenced by the conformational behavior of these compounds in polar and apolar environments. The size and complexity of peptides often limit their bioavailabil...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/acs.jcim.6b00251

    authors: Witek J,Keller BG,Blatter M,Meissner A,Wagner T,Riniker S

    更新日期:2016-08-22 00:00:00

  • Secondary structure characterization based on amino acid composition and availability in proteins.

    abstract::The importance of thorough analyses of the secondary structures in proteins as basic structural units cannot be overemphasized. Although recent computational methods have achieved reasonably high accuracy for predicting secondary structures from amino acid sequences, a simple and fundamental empirical approach to char...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci900452z

    authors: Otaki JM,Tsutsumi M,Gotoh T,Yamamoto H

    更新日期:2010-04-26 00:00:00

  • 3D QSAR methods: Phase and Catalyst compared.

    abstract::The programs Phase and Catalyst HypoGen are compared for their performance in determining three-dimensional quantitative structure-activity relationships. Eight sets of compounds with measured activity were collected from the public literature and partitioned into suitable training and test sets by an automated proced...

    journal_title:Journal of chemical information and modeling

    pub_type: 杂志文章

    doi:10.1021/ci7000082

    authors: Evans DA,Doman TN,Thorner DA,Bodkin MJ

    更新日期:2007-05-01 00:00:00