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Olive LN, Dornshuld EV, Schaefer HF, Tschumper GS. Competition between Solvent···Solvent and Solvent···Solute Interactions in the Microhydration of the Tetrafluoroborate Anion, BF 4-(H 2O) n=1,2,3,4. J Phys Chem A 2023; 127:8806-8820. [PMID: 37774368 DOI: 10.1021/acs.jpca.3c04014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
This study systematically examines the interactions of the tetrafluoroborate anion (BF4-) with up to four water molecules (BF4-(H2O)n=1,2,3,4). Full geometry optimizations and subsequent harmonic vibrational frequency computations are performed using a variety of density functional theory (DFT) methods (B3LYP, B3LYP-D3BJ, and M06-2X) and the MP2 ab initio method with a triple-ζ correlation consistent basis set augmented with diffuse functions on all non-hydrogen atoms (cc-pVTZ for H and aug-cc-pVTZ for B, O, and F; denoted as haTZ). Optimized structures and harmonic vibrational frequencies were also obtained with the CCSD(T) ab initio method and the haTZ basis set for the mono- and dihydrate (n = 1, 2) structures. The 2-body:Many-body (2b:Mb) technique, in which CCSD(T) computations capture the 1- and 2-body contributions to the interactions and MP2 computations recover all higher-order contributions, was used to extend these demanding computations to the tri- and tetrahydrate (n = 3, 4) systems. Four, five, and eight new stationary points have been identified for the di-, tri-, and tetrahydrate systems, respectively. The global minimum of the monohydrate adopts a symmetric double ionic hydrogen bond motif with C2v symmetry and an electronic dissociation energy of 13.17 kcal mol-1 at the CCSD(T)/haTZ level of theory. This strong solvent···solute interaction, however, competes with solute···solute interactions in the lowest-energy BF4-(H2O)n=2,3,4 minima that are not seen in the other di-, tri-, or tetrahydrate minima. The latter interactions help increase the 2b:Mb dissociation energies to more than 26, 41, and 51 kcal mol-1 for n = 2, 3, and 4, respectively. Structures that form hydrogen bonds between the solvating water molecules also exhibit the largest shifts in the harmonic OH stretching frequencies for the waters of hydration. These shifts can exceed -280 cm-1 relative to an isolated H2O molecule at the 2b:Mb/haTZ level of theory.
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Affiliation(s)
- Laura N Olive
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Eric V Dornshuld
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Gregory S Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
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Ramanathan N, Sankaran K, Sundararajan K. Nitrogen: A New Class of π-Bonding Partner in Hetero π-Stacking Interaction. J Phys Chem A 2017; 121:9081-9091. [DOI: 10.1021/acs.jpca.7b08164] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- N. Ramanathan
- Materials Chemistry & Metal Fuel Cycle Group, ‡Homi Bhabha National Institute, Indira Gandhi Center for Atomic Research, Kalpakkam 603102, Tamil Nadu, India
| | - K. Sankaran
- Materials Chemistry & Metal Fuel Cycle Group, ‡Homi Bhabha National Institute, Indira Gandhi Center for Atomic Research, Kalpakkam 603102, Tamil Nadu, India
| | - K. Sundararajan
- Materials Chemistry & Metal Fuel Cycle Group, ‡Homi Bhabha National Institute, Indira Gandhi Center for Atomic Research, Kalpakkam 603102, Tamil Nadu, India
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Copeland KL, Pellock SJ, Cox JR, Cafiero ML, Tschumper GS. Examination of tyrosine/adenine stacking interactions in protein complexes. J Phys Chem B 2013; 117:14001-8. [PMID: 24171662 DOI: 10.1021/jp408027j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The π-stacking interactions between tyrosine amino acid side chains and adenine-bearing ligands are examined. Crystalline protein structures from the protein data bank (PDB) exhibiting face-to-face tyrosine/adenine arrangements were used to construct 20 unique 4-methylphenol/N9-methyladenine (p-cresol/9MeA) model systems. Full geometry optimization of the 20 crystal structures with the M06-2X density functional theory method identified 11 unique low-energy conformations. CCSD(T) complete basis set (CBS) limit interaction energies were estimated for all of the structures to determine the magnitude of the interaction between the two ring systems. CCSD(T) computations with double-ζ basis sets (e.g., 6-31G*(0.25) and aug-cc-pVDZ) indicate that the MP2 method overbinds by as much as 3.07 kcal mol(-1) for the crystal structures and 3.90 kcal mol(-1) for the optimized structures. In the 20 crystal structures, the estimated CCSD(T) CBS limit interaction energy ranges from -4.00 to -6.83 kcal mol(-1), with an average interaction energy of -5.47 kcal mol(-1), values remarkably similar to the corresponding data for phenylalanine/adenine stacking interactions. Geometry optimization significantly increases the interaction energies of the p-cresol/9MeA model systems. The average estimated CCSD(T) CBS limit interaction energy of the 11 optimized structures is 3.23 kcal mol(-1) larger than that for the 20 crystal structures.
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Affiliation(s)
- Kari L Copeland
- Department of Chemistry and Biochemistry, University of Mississippi , University, Mississippi 38677, United States
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Raju RK, Bloom JWG, Wheeler SE. Broad Transferability of Substituent Effects in π-Stacking Interactions Provides New Insights into Their Origin. J Chem Theory Comput 2013; 9:3479-90. [DOI: 10.1021/ct400481r] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Rajesh K. Raju
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Jacob W. G. Bloom
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, United States
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Abstract
Fundamental features of biomolecules, such as their structure, solvation, and crystal packing and even the docking of drugs, rely on noncovalent interactions. Theory can help elucidate the nature of these interactions, and energy component analysis reveals the contributions from the various intermolecular forces: electrostatics, London dispersion terms, induction (polarization), and short-range exchange-repulsion. Symmetry-adapted perturbation theory (SAPT) provides one method for this type of analysis. In this Account, we show several examples of how SAPT provides insight into the nature of noncovalent π-interactions. In cation-π interactions, the cation strongly polarizes electrons in π-orbitals, leading to substantially attractive induction terms. This polarization is so important that a cation and a benzene attract each other when placed in the same plane, even though a consideration of the electrostatic interactions alone would suggest otherwise. SAPT analysis can also support an understanding of substituent effects in π-π interactions. Trends in face-to-face sandwich benzene dimers cannot be understood solely in terms of electrostatic effects, especially for multiply substituted dimers, but SAPT analysis demonstrates the importance of London dispersion forces. Moreover, detailed SAPT studies also reveal the critical importance of charge penetration effects in π-stacking interactions. These effects arise in cases with substantial orbital overlap, such as in π-stacking in DNA or in crystal structures of π-conjugated materials. These charge penetration effects lead to attractive electrostatic terms where a simpler analysis based on atom-centered charges, electrostatic potential plots, or even distributed multipole analysis would incorrectly predict repulsive electrostatics. SAPT analysis of sandwich benzene, benzene-pyridine, and pyridine dimers indicates that dipole/induced-dipole terms present in benzene-pyridine but not in benzene dimer are relatively unimportant. In general, a nitrogen heteroatom contracts the electron density, reducing the magnitude of both the London dispersion and the exchange-repulsion terms, but with an overall net increase in attraction. Finally, using recent advances in SAPT algorithms, researchers can now perform SAPT computations on systems with 200 atoms or more. We discuss a recent study of the intercalation complex of proflavine with a trinucleotide duplex of DNA. Here, London dispersion forces are the strongest contributors to binding, as is typical for π-π interactions. However, the electrostatic terms are larger than usual on a fractional basis, which likely results from the positive charge on the intercalator and its location between two electron-rich base pairs. These cation-π interactions also increase the induction term beyond those of typical noncovalent π-interactions.
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Affiliation(s)
- C. David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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Bera PP, Head-Gordon M, Lee TJ. Association mechanisms of unsaturated C2 hydrocarbons with their cations: acetylene and ethylene. Phys Chem Chem Phys 2013; 15:2012-23. [PMID: 23258256 DOI: 10.1039/c2cp43740f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Partha P Bera
- MS 245-6 NASA Ames Research Center, Moffett Field, Mountain View, California 94035, USA
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Yang J, Waller MP. JACOB: a dynamic database for computational chemistry benchmarking. J Chem Inf Model 2012; 52:3255-62. [PMID: 23157388 DOI: 10.1021/ci300374g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
JACOB (just a collection of benchmarks) is a database that contains four diverse benchmark studies, which in-turn included 72 data sets, with a total of 122,356 individual results. The database is constructed upon a dynamic web framework that allows users to retrieve data from the database via predefined categories. Additional flexibility is made available via user-defined text-based queries. Requested sets of results are then automatically presented as bar graphs, with parameters of the graphs being controllable via the URL. JACOB is currently available at www.wallerlab.org/jacob.
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Affiliation(s)
- Jack Yang
- Theoretische Organische Chemie, Organisch-Chemisches Institut der Westfälische Wilhelms Universität Münster, Corrensstraße 40, 48149 Münster, Germany
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Copeland KL, Tschumper GS. Effects of Heterogeneity in Small π-Type Dimers: Homogeneous and Mixed Dimers of Diacetylene and Cyanogen. J Chem Theory Comput 2012; 8:4279-84. [DOI: 10.1021/ct300644a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kari L. Copeland
- Department of Chemistry
and Biochemistry, University of Mississippi, University, Mississippi
38677-1848, United States
| | - Gregory S. Tschumper
- Department of Chemistry
and Biochemistry, University of Mississippi, University, Mississippi
38677-1848, United States
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Xu Y, Karmakar A, Heberlein WE, Mustafa T, Biris AR, Biris AS. Multifunctional magnetic nanoparticles for synergistic enhancement of cancer treatment by combinatorial radio frequency thermolysis and drug delivery. Adv Healthc Mater 2012. [PMID: 23184783 DOI: 10.1002/adhm.201200079] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Few-layer, carbon-coated, iron (C/Fe) magnetic nanoparticles (MNPs) were synthesized with controlled sizes ranging from 7 to 9 nm. The additional loading of two anti-cancer drugs, doxorubicin and erlotinib, was achieved through - stacking onto the carbon shells. Controlled release of the drugs was successfully triggered by radio frequency (RF) heating or pH variation. Based on the experimental results, C/Fe MNPs act as heat-inducing agents and are able to thermally destroy cancer cells when RF is applied. It was found that the combination of anti-cancer drugs (in particular a low dose of doxorubicin) and RF treatment demonstrates a synergistic effect in inducing cell death in pancreatic cancer cells. Our findings demonstrate that MNPs can be used as highly efficient multimodal nanocarrier agents for an integrated approach to cancer treatment involving triggered delivery of antineoplastic drugs and RF-induced thermal therapy.
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Affiliation(s)
- Yang Xu
- Center for Integrative Nanotechnology Sciences, University of Arkansas at Little Rock, 2801 S. University Ave, AR 72204, USA.
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Sredojević DN, Vojislavljević DZ, Tomić ZD, Zarić SD. Parallel stacking interactions in square-planar transition-metal complexes containing fused chelate and C6-aromatic rings. ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2012; 68:261-5. [DOI: 10.1107/s0108768112012281] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 03/21/2012] [Indexed: 11/10/2022]
Abstract
Stacking interactions in the crystal structures of square-planar transition metal complexes from the Cambridge Structural Database with five- and six-membered chelate rings fused with C6-arom rings (arom = aromatic) were analyzed. The distribution of distances between the closest C6-arom–C6-arom and C6-arom–chelate contacts shows that in a large fraction of the intermolecular interactions the C6-arom ring of one molecule is closer to the chelate than to the C6-arom ring of the other molecule. These results indicate a possible preference of the C6-arom ring to form stacking contacts with the chelate rings. The preference is ubiquitous and does not depend on the metal type.
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12
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Carrell EJ, Thorne CM, Tschumper GS. Basis set dependence of higher-order correlation effects in π-type interactions. J Chem Phys 2012; 136:014103. [PMID: 22239765 DOI: 10.1063/1.3671950] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The basis set dependence of higher-order correlation effects on π-type interaction energies was examined by scanning the potential energy surfaces of five dimer systems. The dimers of acetylene (H-C≡C-H), diacetylene (H-C≡C-C≡C-H), cyanogen (N≡C-C≡N), diphosphorous (P≡P), and 1,4-diphosphabutadiyne (P≡C-C≡P) were studied in three different configurations: cross, parallel-displaced, and t-shaped. More than 800 potential energy curves (PECs) were generated by computing the interaction energies for all 15 dimer configurations over a range of intermolecular distances with the MP2, coupled-cluster single double (CCSD), and coupled-cluster single double triple (CCSD(T)) methods in conjunction with 21 basis sets ranging from a small 6-31G*(0.25) split-valence basis set to a large aug-cc-pVQZ correlation consistent basis set. Standard extrapolation techniques were also used to construct MP2, CCSD, and CCSD(T) complete basis set (CBS) limit PECs as well as CBS limit higher-order correlation corrections based on the differences between CCSD(T) and MP2 interaction energies, denoted δ(MP2)(CCSD(T)), and the corresponding differences between CCSD(T) and CCSD interactions energies, denoted δ(CCSD)(CCSD(T)). Double-ζ basis sets struggled to reproduce the former but provided quite reasonable descriptions of the latter as long as diffuse functions were included. The aug-cc-pVDZ basis deviated from the δ(CCSD)(CCSD(T)) CBS limit by only 0.06 kcal mol(-1) on average and never by more than 0.24 kcal mol(-1), whereas the corresponding deviations were approximately twice that for the δ(MP2)(CCSD(T)) term. While triple-ζ basis sets typically improved results, only aug-cc-pVTZ provided appreciable improvement over utilizing the aug-cc-pVDZ basis set to compute δ(CCSD)(CCSD(T)). Counterpoise (CP) corrections were also applied to all double- and triple-ζ basis sets, but they rarely yielded a better description of these higher-order correlation effects. CP corrections only consistently improved results when the aug-cc-pVDZ basis set was used to compute δ(MP2)(CCSD(T)), yielding mean and maximum absolute deviations from the CBS values of 0.10 and 0.39 kcal mol(-1), respectively, for all five dimer systems.
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Affiliation(s)
- Emily J Carrell
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677-1848, USA
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14
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Ebrahimi A, Khorassani SH, Abedini S. The mutual relationship between H-bonding and π-stacking interactions: the estimation of individual binding energies in the phenylalanine:G ··· C ternary complex. Mol Phys 2011. [DOI: 10.1080/00268976.2011.609144] [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]
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15
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Ghosh D, Kosenkov D, Vanovschi V, Williams CF, Herbert JM, Gordon MS, Schmidt MW, Slipchenko LV, Krylov AI. Noncovalent interactions in extended systems described by the effective fragment potential method: theory and application to nucleobase oligomers. J Phys Chem A 2010; 114:12739-54. [PMID: 21067134 DOI: 10.1021/jp107557p] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The implementation of the effective fragment potential (EFP) method within the Q-CHEM electronic structure package is presented. The EFP method is used to study noncovalent π-π and hydrogen-bonding interactions in DNA strands. Since EFP is a computationally inexpensive alternative to high-level ab initio calculations, it is possible to go beyond the dimers of nucleic acid bases and to investigate the asymptotic behavior of different components of the total interaction energy. The calculations demonstrated that the dispersion energy is a leading component in π-stacked oligomers of all sizes. Exchange-repulsion energy also plays an important role. The contribution of polarization is small in these systems, whereas the magnitude of electrostatics varies. Pairwise fragment interactions (i.e., the sum of dimer binding energies) were found to be a good approximation for the oligomer energy.
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Affiliation(s)
- Debashree Ghosh
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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Sanders JM. Optimal π-Stacking Interaction Energies in Parallel-Displaced Aryl/Aryl Dimers are Predicted by the Dimer Heavy Atom Count. J Phys Chem A 2010; 114:9205-11. [DOI: 10.1021/jp912094q] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- John M. Sanders
- Department of Chemistry Modeling and Informatics, Merck Research Laboratories, West Point, Pennsylvania 19486
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17
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Geronimo I, Lee EC, Singh NJ, Kim KS. How Different are Electron-Rich and Electron-Deficient π Interactions? J Chem Theory Comput 2010; 6:1931-4. [DOI: 10.1021/ct100182u] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Inacrist Geronimo
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - Eun Cheol Lee
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - N. Jiten Singh
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, Pohang, 790-784, Korea
| | - Kwang S. Kim
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, Pohang, 790-784, Korea
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18
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Peverati R, Baldridge KK. Implementation and Optimization of DFT-D/COSab with Respect to Basis Set and Functional: Application to Polar Processes of Furfural Derivatives in Solution. J Chem Theory Comput 2009; 5:2772-86. [DOI: 10.1021/ct900363n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Roberto Peverati
- University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Kim K. Baldridge
- University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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Sancho-García JC, Pérez-Jiménez AJ. Assessment of double-hybrid energy functionals for π-conjugated systems. J Chem Phys 2009; 131:084108. [DOI: 10.1063/1.3212881] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Hohenstein EG, Sherrill CD. Effects of heteroatoms on aromatic pi-pi interactions: benzene-pyridine and pyridine dimer. J Phys Chem A 2009; 113:878-86. [PMID: 19132847 DOI: 10.1021/jp809062x] [Citation(s) in RCA: 250] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Heteroatoms are found in many noncovalent complexes which are of biological importance. The effect of heteroatoms on pi-pi interactions is assessed via highly accurate quantum chemical computations for the two simplest cases of interactions between aromatic molecules containing heteroatoms, namely, benzene-pyridine and pyridine dimer. Benchmark quality estimated coupled-cluster through perturbative triples [CCSD(T)] binding energies are computed near the complete basis set limit. Comparisons to the benzene dimer are made to determine the contributions from heteroatoms. The presence of a heteroatom reduces the spatial extent of the pi-electron cloud and polarizability of pyridine as compared to benzene. As a result, the magnitude of the dispersion, exchange, and induction interactions in benzene-pyridine and pyridine dimer is generally reduced as compared to those for the benzene dimer. Benzene-pyridine and pyridine dimer bind more strongly than the benzene dimer in several configurations, and in contrast to the benzene dimer, parallel-displaced configurations can be significantly preferred over T-shaped configurations. Hydrogens para to a heteroatom are more effective "pi-hydrogen bond" donors, but aromatic rings with heteroatoms are worse "pi-hydrogen bond" acceptors.
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Affiliation(s)
- Edward G Hohenstein
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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Bates DM, Tschumper GS. CCSD(T) Complete Basis Set Limit Relative Energies for Low-Lying Water Hexamer Structures. J Phys Chem A 2009; 113:3555-9. [DOI: 10.1021/jp8105919] [Citation(s) in RCA: 176] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Desiree M. Bates
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677-1848
| | - Gregory S. Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677-1848
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Peverati R, Baldridge KK. Implementation and Performance of DFT-D with Respect to Basis Set and Functional for Study of Dispersion Interactions in Nanoscale Aromatic Hydrocarbons. J Chem Theory Comput 2008; 4:2030-48. [DOI: 10.1021/ct800252z] [Citation(s) in RCA: 149] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Kim K Baldridge
- University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich
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Copeland KL, Anderson JA, Farley AR, Cox JR, Tschumper GS. Probing phenylalanine/adenine pi-stacking interactions in protein complexes with explicitly correlated and CCSD(T) computations. J Phys Chem B 2008; 112:14291-5. [PMID: 18922031 DOI: 10.1021/jp805528v] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To examine the effects of pi-stacking interactions between aromatic amino acid side chains and adenine bearing ligands in crystalline protein structures, 26 toluene/(N9-methyl)adenine model configurations have been constructed from protein/ligand crystal structures. Full geometry optimizations with the MP2 method cause the 26 crystal structures to collapse to six unique structures. The complete basis set (CBS) limit of the CCSD(T) interaction energies has been determined for all 32 structures by combining explicitly correlated MP2-R12 computations with a correction for higher-order correlation effects from CCSD(T) calculations. The CCSD(T) CBS limit interaction energies of the 26 crystal structures range from -3.19 to -6.77 kcal mol (-1) and average -5.01 kcal mol (-1). The CCSD(T) CBS limit interaction energies of the optimized complexes increase by roughly 1.5 kcal mol (-1) on average to -6.54 kcal mol (-1) (ranging from -5.93 to -7.05 kcal mol (-1)). Corrections for higher-order correlation effects are extremely important for both sets of structures and are responsible for the modest increase in the interaction energy after optimization. The MP2 method overbinds the crystal structures by 2.31 kcal mol (-1) on average compared to 4.50 kcal mol (-1) for the optimized structures.
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Affiliation(s)
- Kari L Copeland
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, USA
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