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Riley KE, Hobza P. The relative roles of electrostatics and dispersion in the stabilization of halogen bonds. Phys Chem Chem Phys 2014; 15:17742-51. [PMID: 24067893 DOI: 10.1039/c3cp52768a] [Citation(s) in RCA: 113] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this work we highlight recent work aimed at the characterization of halogen bonds. Here we discuss the origins of the σ-hole, the modulation of halogen bond strength by changing of neighboring chemical groups (i.e. halogen bond tuning), the performance of various computational methods in treating halogen bonds, and the strength and character of the halogen bond, the dihalogen bond, and two hydrogen bonds in bromomethanol dimers (which serve as model complexes) are compared. Symmetry adapted perturbation theory analysis of halogen bonding complexes indicates that halogen bonds strongly depend on both dispersion and electrostatics. The electrostatic interaction that occurs between the halogen σ-hole and the electronegative halogen bond donor is responsible for the high degree of directionality exhibited by halogen bonds. Because these noncovalent interactions have a strong dispersion component, it is important that the computational method used to treat a halogen bonding system be chosen very carefully, with correlated methods (such as CCSD(T)) being optimal. It is also noted here that most forcefield-based molecular mechanics methods do not describe the halogen σ-hole, and thus are not suitable for treating systems with halogen bonds. Recent attempts to improve the molecular mechanics description of halogen bonds are also discussed.
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102
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Sedlak R, Deepa P, Hobza P. Why Is the L-Shaped Structure of X2···X2 (X = F, Cl, Br, I) Complexes More Stable Than Other Structures? J Phys Chem A 2014; 118:3846-3855. [DOI: 10.1021/jp502648e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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103
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Deepa P, Sedlak R, Hobza P. On the origin of the substantial stabilisation of the electron-donor 1,3-dithiole-2-thione-4-carboxyclic acid···I2 and DABCO···I2 complexes. Phys Chem Chem Phys 2014; 16:6679-86. [PMID: 24584418 DOI: 10.1039/c4cp00055b] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The stabilisation energies of the crystal structures of 1,3-dithiole-2-thione-4-carboxyclic acid···I2 and DABCO···I2 complexes determined by the CCSD(T)/CBS method are very large and exceed 8 and 15 kcal mol(-1), respectively. The DFT-D method (B97-D3/def2-QZVP) strongly overestimates these stabilisation energies, which support the well-known fact that the DFT-D method is not very applicable to the study of charge-transfer complexes. On the other hand, the M06-2X/def2-QZVP method provides surprisingly reliable energies. A DFT-SAPT analysis has shown that a substantial stabilisation of these complexes arises from the charge-transfer energy included in the induction energy and that the respective induction energy is much larger than that of other non-covalently bound complexes. The total stabilisation energies of the complexes mentioned as well as of those where iodine has been replaced by lighter halogens (Br2 and Cl2) or by hetero systems (IF, ICH3, N2) correlate well with the magnitude of the σ-hole (Vs,max value) as well as with the LUMO energy. The nature of the stabilisation of all complexes between both electron donors and X2 (X = I, Br, Cl, N) systems is explained by the magnitude of the σ-hole but surprisingly also by the values of the electric quadrupole moment of these systems. Evidently, the nature of the stabilisation of halogen-bonded complexes between electron donors and systems where the first non-zero electric multipole moment is the quadrupole moment can be explained not only by the recently introduced concept of the σ-hole but also by the classical concept of electric quadrupole moments.
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104
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Tewari AK, Srivastava P, Singh VP, Singh P, Kumar R, Khanna RS, Srivastava P, Gnanasekaran R, Hobza P. Selective induced polarization through electron transfer in acetone and pyrazole ester derivatives via C–H⋯OC interaction. NEW J CHEM 2014. [DOI: 10.1039/c4nj00679h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A set of organic compounds (pyrazole ester derivatives,viz.5-[3-(substituted)-propoxy]-3-methyl-1-phenyl-1H-pyrazole-4-carboxylic acid methyl ester and 5-[2-(substituted)-ethoxy]-3-methyl-1-phenyl-1H-pyrazole-4-carboxylic acid methyl ester) was synthesized and their affinity and stability towards the acetone molecule were tested by NMR.
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105
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Lazar P, Granatier J, Klimeš J, Hobza P, Otyepka M. The nature of bonding and electronic properties of graphene and benzene with iridium adatoms. Phys Chem Chem Phys 2014; 16:20818-27. [DOI: 10.1039/c4cp02608j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The strong correlation effects contribute to the opening of the band gap in graphene covered with the Ir adatoms.
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106
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Kolář M, Hostaš J, Hobza P. The strength and directionality of a halogen bond are co-determined by the magnitude and size of the σ-hole. Phys Chem Chem Phys 2014; 16:9987-96. [DOI: 10.1039/c3cp55188a] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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107
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Demovičová L, Hobza P, Řezáč J. Evaluation of composite schemes for CCSDT(Q) calculations of interaction energies of noncovalent complexes. Phys Chem Chem Phys 2014; 16:19115-21. [DOI: 10.1039/c4cp02617a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Evaluation of composite schemes for CCSDT(Q) calculations of interaction energies of noncovalent complexes.
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108
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Kolář MH, Carloni P, Hobza P. Statistical analysis of σ-holes: a novel complementary view on halogen bonding. Phys Chem Chem Phys 2014; 16:19111-4. [DOI: 10.1039/c4cp02621g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Halogen σ-hole characteristics are defined and their typical values are provided based on an extensive analysis of more than 2500 molecules from the ZINC database.
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109
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Kolář MH, Deepa P, Ajani H, Pecina A, Hobza P. Characteristics of a σ-Hole and the Nature of a Halogen Bond. Top Curr Chem (Cham) 2014; 359:1-25. [DOI: 10.1007/128_2014_606] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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110
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Pecina A, Lepšík M, Řezáč J, Brynda J, Mader P, Řezáčová P, Hobza P, Fanfrlík J. QM/MM Calculations Reveal the Different Nature of the Interaction of Two Carborane-Based Sulfamide Inhibitors of Human Carbonic Anhydrase II. J Phys Chem B 2013; 117:16096-104. [DOI: 10.1021/jp410216m] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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111
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Fanfrlík J, Brahmkshatriya PS, Řezáč J, Jílková A, Horn M, Mareš M, Hobza P, Lepšík M. Quantum mechanics-based scoring rationalizes the irreversible inactivation of parasitic Schistosoma mansoni cysteine peptidase by vinyl sulfone inhibitors. J Phys Chem B 2013; 117:14973-82. [PMID: 24195769 DOI: 10.1021/jp409604n] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The quantum mechanics (QM)-based scoring function that we previously developed for the description of noncovalent binding in protein-ligand complexes has been modified and extended to treat covalent binding of inhibitory ligands. The enhancements are (i) the description of the covalent bond breakage and formation using hybrid QM/semiempirical QM (QM/SQM) restrained optimizations and (ii) the addition of the new ΔG(cov)' term to the noncovalent score, describing the "free" energy difference between the covalent and noncovalent complexes. This enhanced QM-based scoring function is applied to a series of 20 vinyl sulfone-based inhibitory compounds inactivating the cysteine peptidase cathepsin B1 of the Schistosoma mansoni parasite (SmCB1). The available X-ray structure of the SmCB1 in complex with a potent vinyl sulfone inhibitor K11017 is used as a template to build the other covalently bound complexes and to model the derived noncovalent complexes. We present the correlation of the covalent score and its constituents with the experimental binding data. Four outliers are identified. They contain bulky R1' substituents structurally divergent from the template, which might induce larger protein rearrangements than could be accurately modeled. In summary, we propose a new computational approach and an optimal protocol for the rapid evaluation and prospective design of covalent inhibitors with a conserved binding mode.
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112
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Melicherčík M, Pitoňák M, Kellö V, Hobza P, Neogrády P. Off-Center Gaussian Functions, an Alternative Atomic Orbital Basis Set for Accurate Noncovalent Interaction Calculations of Large Systems. J Chem Theory Comput 2013; 9:5296-304. [DOI: 10.1021/ct400692b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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113
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Fanfrlík J, Kolář M, Kamlar M, Hurný D, Ruiz FX, Cousido-Siah A, Mitschler A, Řezáč J, Munusamy E, Lepšík M, Matějíček P, Veselý J, Podjarny A, Hobza P. Modulation of aldose reductase inhibition by halogen bond tuning. ACS Chem Biol 2013; 8:2484-92. [PMID: 23988122 DOI: 10.1021/cb400526n] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In this paper, we studied a designed series of aldose reductase (AR) inhibitors. The series was derived from a known AR binder, which had previously been shown to form a halogen bond between its bromine atom and the oxygen atom of the Thr-113 side chain of AR. In the series, the strength of the halogen bond was modulated by two factors, namely bromine-iodine substitution and the fluorination of the aromatic ring in several positions. The role of the single halogen bond in AR-ligand binding was elucidated by advanced binding free energy calculations involving the semiempirical quantum chemical Hamiltonian. The results were complemented with ultrahigh-resolution X-ray crystallography and IC50 measurements. All of the AR inhibitors studied were shown by X-ray crystallography to bind in an identical manner. Further, it was demonstrated that it was possible to decrease the IC50 value by about 1 order of magnitude by tuning the strength of the halogen bond by a monoatomic substitution. The calculations revealed that the protein-ligand interaction energy increased upon the substitution of iodine for bromine or upon the addition of electron-withdrawing fluorine atoms to the ring. However, the effect on the binding affinity was found to be more complex due to the change of the solvation/desolvation properties within the ligand series. The study shows that it is possible to modulate the strength of a halogen bond in a protein-ligand complex as was designed based on the previous studies of low-molecular-weight complexes.
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114
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Dubecký M, Jurečka P, Derian R, Hobza P, Otyepka M, Mitas L. Quantum Monte Carlo Methods Describe Noncovalent Interactions with Subchemical Accuracy. J Chem Theory Comput 2013; 9:4287-92. [DOI: 10.1021/ct4006739] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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115
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Sedlak R, Janowski T, Pitoňák M, Řezáč J, Pulay P, Hobza P. The accuracy of quantum chemical methods for large noncovalent complexes. J Chem Theory Comput 2013; 9:3364-3374. [PMID: 24098094 PMCID: PMC3789125 DOI: 10.1021/ct400036b] [Citation(s) in RCA: 255] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We evaluate the performance of the most widely used wavefunction, density functional theory, and semiempirical methods for the description of noncovalent interactions in a set of larger, mostly dispersion-stabilized noncovalent complexes (the L7 data set). The methods tested include MP2, MP3, SCS-MP2, SCS(MI)-MP2, MP2.5, MP2.X, MP2C, DFT-D, DFT-D3 (B3-LYP-D3, B-LYP-D3, TPSS-D3, PW6B95-D3, M06-2X-D3) and M06-2X, and semiempirical methods augmented with dispersion and hydrogen bonding corrections: SCC-DFTB-D, PM6-D, PM6-DH2 and PM6-D3H4. The test complexes are the octadecane dimer, the guanine trimer, the circumcoronene…adenine dimer, the coronene dimer, the guanine-cytosine dimer, the circumcoronene…guanine-cytosine dimer, and an amyloid fragment trimer containing phenylalanine residues. The best performing method is MP2.5 with relative root mean square deviation (rRMSD) of 4 %. It can thus be recommended as an alternative to the CCSD(T)/CBS (alternatively QCISD(T)/CBS) benchmark for molecular systems which exceed current computational capacity. The second best non-DFT method is MP2C with rRMSD of 8 %. A method with the most favorable "accuracy/cost" ratio belongs to the DFT family: BLYP-D3, with an rRMSD of 8 %. Semiempirical methods deliver less accurate results (the rRMSD exceeds 25 %). Nevertheless, their absolute errors are close to some much more expensive methods such as M06-2X, MP2 or SCS(MI)-MP2, and thus their price/performance ratio is excellent.
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Šimová L, Řezáč J, Hobza P. Convergence of the Interaction Energies in Noncovalent Complexes in the Coupled-Cluster Methods Up to Full Configuration Interaction. J Chem Theory Comput 2013; 9:3420-8. [DOI: 10.1021/ct4002762] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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117
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Trnka J, Sedlak R, Kolář M, Hobza P. Differences in the Sublimation Energy of Benzene and Hexahalogenbenzenes Are Caused by Dispersion Energy. J Phys Chem A 2013; 117:4331-7. [DOI: 10.1021/jp401961g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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118
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Kolář M, Fanfrlík J, Lepšík M, Forti F, Luque FJ, Hobza P. Assessing the accuracy and performance of implicit solvent models for drug molecules: conformational ensemble approaches. J Phys Chem B 2013; 117:5950-62. [PMID: 23600402 DOI: 10.1021/jp402117c] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The accuracy and performance of implicit solvent methods for solvation free energy calculations were assessed on a set of 20 neutral drug molecules. Molecular dynamics (MD) provided ensembles of conformations in water and water-saturated octanol. The solvation free energies were calculated by popular implicit solvent models based on quantum mechanical (QM) electronic densities (COSMO-RS, MST, SMD) as well as on molecular mechanical (MM) point-charge models (GB, PB). The performance of the implicit models was tested by a comparison with experimental water-octanol transfer free energies (ΔG(ow)) by using single- and multiconformation approaches. MD simulations revealed difficulties in a priori estimation of the flexibility features of the solutes from simple structural descriptors, such as the number of rotatable bonds. An increasing accuracy of the calculated ΔG(ow) was observed in the following order: GB1 ~ PB < GB7 ≪ MST < SMD ~ COSMO-RS with a clear distinction identified between MM- and QM-based models, although for the set excluding three largest molecules, the differences among COSMO-RS, MST, and SMD were negligible. It was shown that the single-conformation approach applied to crystal geometries provides a rather accurate estimate of ΔG(ow) for rigid molecules yet fails completely for the flexible ones. The multiconformation approaches improved the performance, but only when the deformation contribution was ignored. It was revealed that for large-scale calculations on small molecules a recent GB model, GB7, provided a reasonable accuracy/speed ratio. In conclusion, the study contributes to the understanding of solvation free energy calculations for physical and medicinal chemistry applications.
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119
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Hostaš J, Řezáč J, Hobza P. On the performance of the semiempirical quantum mechanical PM6 and PM7 methods for noncovalent interactions. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.02.069] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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120
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Riley KE, Hobza P. On the importance and origin of aromatic interactions in chemistry and biodisciplines. Acc Chem Res 2013; 46:927-36. [PMID: 22872015 DOI: 10.1021/ar300083h] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aromatic systems contain both σ- and π-electrons, which in turn constitute σ- and π-molecular orbitals (MOs). In discussing the properties of these systems, researchers typically refer to the highest occupied and lowest unoccupied MOs, which are π MOs. The characteristic properties of aromatic systems, such as their low ionization potentials and electron affinities, high polarizabilities and stabilities, and small band gaps (in spectroscopy called the N → V1 space), can easily be explained based on their electronic structure. These one-electron properties point to characteristic features of how aromatic systems interact with each other. Unlike hydrogen bonding systems, which primarily interact through electrostatic forces, complexes containing aromatic systems, especially aromatic stacked pairs, are predominantly stabilized by dispersion attraction. The stabilization energy in the benzene dimer is rather small (~2.5 kcal/mol) but strengthens with heteroatom substitution. The stacked interaction of aromatic nucleic acid bases is greater than 10 kcal/mol, and for the most stable stacked pair, guanine and cytosine, it reaches approximately 17 kcal/mol. Although these values do not equal the planar H-bonded interactions of these bases (~29 kcal/mol), stacking in DNA is more frequent than H-bonding and, unlike H-bonding, is not significantly weakened when passing from the gas phase to a water environment. Consequently, the stacking of aromatic systems represents the leading stabilization energy contribution in biomacromolecules and in related nanosystems. Therefore stacking (dispersion) interactions predominantly determine the double helical structure of DNA, which underlies its storage and transfer of genetic information. Similarly, dispersion is the dominant contributor to attractive interactions involving aromatic amino acids within the hydrophobic core of a protein, which is critical for folding. Therefore, understanding the nature of aromatic interactions, which depend greatly on quantum mechanical (QM) calculations, is of key importance in biomolecular science. This Account shows that accurate binding energies for aromatic complexes should be based on computations made at the (estimated) CCSD(T)/complete basis set limit (CBS) level of theory. This method is the least computationally intensive one that can give accurate stabilization energies for all common classes of noncovalent interactions (aromatic-aromatic, H-bonding, ionic, halogen bonding, charge-transfer, etc.). These results allow for direct comparison of binding energies between different interaction types. Conclusions based on lower-level QM calculations should be considered with care.
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121
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Řezáč J, Hobza P. Describing Noncovalent Interactions beyond the Common Approximations: How Accurate Is the “Gold Standard,” CCSD(T) at the Complete Basis Set Limit? J Chem Theory Comput 2013; 9:2151-5. [DOI: 10.1021/ct400057w] [Citation(s) in RCA: 314] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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122
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S. Brahmkshatriya P, Dobes P, Fanfrlik J, Rezac J, Paruch K, Bronowska A, LepsÃk M, Hobza P. Quantum Mechanical Scoring: Structural and Energetic Insights into Cyclin-Dependent Kinase 2 Inhibition by Pyrazolo[1,5-a]pyrimidines. Curr Comput Aided Drug Des 2013. [DOI: 10.2174/157340913804998784] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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123
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Granatier J, Dubecký M, Lazar P, Otyepka M, Hobza P. Spin-Crossing in an Organometallic Pt–Benzene Complex. J Chem Theory Comput 2013; 9:1461-8. [DOI: 10.1021/ct400016c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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124
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Lazar P, Zhang S, Safářová K, Li Q, Froning JP, Granatier J, Hobza P, Zbořil R, Besenbacher F, Dong M, Otyepka M. Quantification of the interaction forces between metals and graphene by quantum chemical calculations and dynamic force measurements under ambient conditions. ACS NANO 2013; 7:1646-1651. [PMID: 23346897 DOI: 10.1021/nn305608a] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The two-dimensional material graphene has numerous potential applications in nano(opto)electronics, which inevitably involve metal graphene interfaces.Theoretical approaches have been employed to examine metal graphene interfaces, but experimental evidence is currently lacking. Here, we combine atomic force microscopy (AFM) based dynamic force measurements and density functional theory calculations to quantify the interaction between metal-coated AFM tips and graphene under ambient conditions. The results show that copper has the strongest affinity to graphene among the studied metals (Cu, Ag, Au, Pt, Si), which has important implications for the construction of a new generation of electronic devices. Observed differences in the nature of the metal-graphene bonding are well reproduced by the calculations, which included nonlocal Hartree-Fock exchange and van der Waals effects.
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S. Brahmkshatriya P, Dobes P, Fanfrlik J, Rezac J, Paruch K, Bronowska A, Lepsík M, Hobza P. Quantum Mechanical Scoring: Structural and Energetic Insights into Cyclin-Dependent Kinase 2 Inhibition by Pyrazolo[1,5-a]pyrimidines. Curr Comput Aided Drug Des 2013; 9:118-29. [DOI: 10.2174/1573409911309010011] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 02/10/2012] [Accepted: 11/02/2012] [Indexed: 11/22/2022]
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