1
|
Jensen F. Basis Set Superposition Errors Are Partly Basis Set Imbalances. J Chem Theory Comput 2024; 20:767-774. [PMID: 38174405 DOI: 10.1021/acs.jctc.3c01156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
When calculating fragment interaction energies by electronic structure methods employing medium-sized atom-centered basis sets, it is often observed that the effect is systematically overestimated. The common interpretation is that the systematic error arises because the basis set for the complex is more complete than for the isolated fragments, and this is denoted basis set superposition errors. It has been observed, however, that the interaction energy in some cases is underestimated, which defies the interpretation in terms of basis set completeness, and instead suggests that the effect partly is due to basis set imbalance. The imbalance can be removed by explicit optimization of the basis sets for each structure, and it is shown that this to a significant extent reduces the systematic overestimation attributed to basis set superposition error.
Collapse
Affiliation(s)
- Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
| |
Collapse
|
2
|
Pitteloud Q, Wind P, Jensen SR, Frediani L, Jensen F. Quantifying Intramolecular Basis Set Superposition Errors. J Chem Theory Comput 2023; 19:5863-5871. [PMID: 37595013 DOI: 10.1021/acs.jctc.3c00693] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Abstract
We show that medium-sized Gaussian basis sets lead to significant intramolecular basis set superposition errors at Hartree-Fock and density functional levels of theory, with artificial stabilization of compact over extended conformations for a 186 atom deca-peptide. Errors of ∼80 and ∼10 kJ/mol are observed, with polarized double zeta and polarized triple zeta quality basis sets, respectively. Two different procedures for taking the basis set superposition error into account are tested. While both reduce the error, it appears that polarized quadruple zeta basis sets are required to reduce the error below a few kJ/mol. Alternatively, the basis set superposition error can be eliminated using multiresolution methods based on Multiwavelets.
Collapse
Affiliation(s)
- Quentin Pitteloud
- Hylleraas Centre, Department of Chemistry, UiT the Arctic University of Norway, Tromsø N-9037, Norway
| | - Peter Wind
- Hylleraas Centre, Department of Chemistry, UiT the Arctic University of Norway, Tromsø N-9037, Norway
| | - Stig Rune Jensen
- Hylleraas Centre, Department of Chemistry, UiT the Arctic University of Norway, Tromsø N-9037, Norway
| | - Luca Frediani
- Hylleraas Centre, Department of Chemistry, UiT the Arctic University of Norway, Tromsø N-9037, Norway
| | - Frank Jensen
- Department of Chemistry, Aarhus University, Aarhus DK-8000, Denmark
| |
Collapse
|
3
|
Watanabe K, Segawa Y, Itami K. A theoretical study on the strain energy of helicene-containing carbon nanobelts. Chem Commun (Camb) 2020; 56:15044-15047. [PMID: 33196074 DOI: 10.1039/d0cc06373h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this study, the theoretical analysis of the strain energy of helicene-containing carbon nanobelts is reported. It was found that the combined method of linear regression analysis and suitable homodesmotic reactions can successfully estimate the strain energies of various helicene-containing carbon nanobelts including previously synthesized chiral (18,12) carbon nanobelts.
Collapse
Affiliation(s)
- Kosuke Watanabe
- Graduate School of Science, Nagoya University, Chikusa, Nagoya 464-8602, Japan.
| | | | | |
Collapse
|
4
|
Oniki J, Moriuchi T, Kamochi K, Tobisu M, Amaya T. Linear [3]Spirobifluorenylene: An S-Shaped Molecular Geometry of p-Oligophenyls. J Am Chem Soc 2019; 141:18238-18245. [DOI: 10.1021/jacs.9b09179] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Jumpei Oniki
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Toshiyuki Moriuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-oka, Suita, Osaka 565-0871, Japan
- Division of Molecular Materials Science, Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Kosuke Kamochi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Mamoru Tobisu
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Toru Amaya
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada-oka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
5
|
Tuca E, Paci I. Structural analysis of helicene molecules adsorbed on symmetric surfaces. Phys Chem Chem Phys 2019; 21:9189-9199. [PMID: 30949648 DOI: 10.1039/c9cp00284g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Helicenes are chiral polyaromatic hydrocarbon molecules which self-assemble into ordered monolayers on solid substrates, and are of current interest in the study of supramolecular systems and the development of smart materials. In this work we investigate the geometry of helicene monomers and stacked dimers on (111) facets of coinage metals. The geometry of the adsorbed molecules is shaped by the coupling of intermolecular dispersive forces, intramolecular steric repulsion between end rings and surface-molecule interactions. Thus, binding and stereospecificity outcomes vary broadly depending on the identity of molecule/surface pair. Overall, homochiral interactions are found to be more effective than heterochiral stacking, due to a better fit between the helical structures in like dimers. On a surface, this effect is enhanced by the flattening of surface-proximal molecular rings. However, our results show that the "sandwich" effect of the second molecular layer increases molecular footprints in the first layer, with potentially large implications in monolayer organization and surface commensuration.
Collapse
Affiliation(s)
- Emilian Tuca
- Department of Chemistry and Centre for Advanced Materials and Related Technologies, University of Victoria, PO Box 1700, 3800 Finnerty Road, Victoria, BC V8W 2Y2, Canada.
| | | |
Collapse
|
6
|
Sharapa DI, Genaev A, Cavallo L, Minenkov Y. A Robust and Cost‐Efficient Scheme for Accurate Conformational Energies of Organic Molecules. Chemphyschem 2018; 20:92-102. [DOI: 10.1002/cphc.201801063] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Dmitry I. Sharapa
- Institute of Catalysis Research and TechnologyKarlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz Platz 1 Eggenstein-Leopoldshafen D-76344 Germany
| | - Alexander Genaev
- Vorozhtsov Novosibirsk Institute of Organic Chemistry Academician Lavrent'ev Ave., 9 Novosibirsk 630090 Russian Federation
| | - Luigi Cavallo
- KAUST Catalysis Center (KCC)King Abdullah University of Science and Technology Thuwal- 23955-6900 Saudi Arabia
| | - Yury Minenkov
- Moscow Institute of Physics and Technology Institutskiy Pereulok 9, Dolgoprudny Moscow Region 141700 Russia
| |
Collapse
|
7
|
Capobianco A, Velardo A, Peluso A. Single-Stranded DNA Oligonucleotides Retain Rise Coordinates Characteristic of Double Helices. J Phys Chem B 2018; 122:7978-7989. [PMID: 30070843 DOI: 10.1021/acs.jpcb.8b04542] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structures of single-stranded DNA oligonucleotides from dimeric to hexameric sequences have been thoroughly investigated. Computations performed at the density functional level of theory including dispersion forces and solvation show that single-stranded helices adopt conformations very close to crystallographic B-DNA, with rise coordinates amounting up to 3.3 Å. Previous results, suggesting that single strands should be shorter than double helices, largely originated from the incompleteness of the adopted basis set. Although sensible deviations with respect to standard B-DNA are predicted, computations indicate that sequences rich in stacked adenines are the most ordered ones, favoring the B-DNA pattern and inducing regular arrangements also on flanking nucleobases. Several structural properties of double helices rich in adenine are indeed already reflected by the corresponding single strands.
Collapse
Affiliation(s)
- Amedeo Capobianco
- Dipartimento di Chimica e Biologia "A. Zambelli" , Università di Salerno , Via Giovanni Paolo II , I-84084 Fisciano (SA) , Italy
| | - Amalia Velardo
- Dipartimento di Chimica e Biologia "A. Zambelli" , Università di Salerno , Via Giovanni Paolo II , I-84084 Fisciano (SA) , Italy
| | - Andrea Peluso
- Dipartimento di Chimica e Biologia "A. Zambelli" , Università di Salerno , Via Giovanni Paolo II , I-84084 Fisciano (SA) , Italy
| |
Collapse
|
8
|
Sirianni DA, Alenaizan A, Cheney DL, Sherrill CD. Assessment of Density Functional Methods for Geometry Optimization of Bimolecular van der Waals Complexes. J Chem Theory Comput 2018; 14:3004-3013. [PMID: 29763302 DOI: 10.1021/acs.jctc.8b00114] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We explore the suitability of three popular density functionals (B97-D3, B3LYP-D3, M05-2X) for producing accurate equilibrium geometries of van der Waals (vdW) complexes with diverse binding motifs. For these functionals, optimizations using Dunning's aug-cc-pVDZ basis set best combine accuracy and a reasonable computational expense. Each DFT/aug-cc-pVDZ combination produces optimized equilibrium geometries for 21 small vdW complexes of organic molecules (up to four non-hydrogen atoms total) that agree with high-level CCSD(T)/CBS reference geometries to within ±0.1 Å for the averages of the center-of-mass displacement and the mean least root-mean-squared displacement. The DFT/aug-cc-pVDZ combinations are also able to reproduce the optimal center-of-mass displacements interpolated from CCSD(T)/CBS radial potential energy surfaces in both NBC7x and HBC6 test sets to within ±0.1 Å. We therefore conclude that each of these denisty functional methods, together with the aug-cc-pVDZ basis set, is suitable for producing equilibrium geometries of generic nonbonded complexes.
Collapse
Affiliation(s)
- Dominic A Sirianni
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332-0400 , United States
| | - Asem Alenaizan
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry , Georgia Institute of Technology , Atlanta , Georgia 30332-0400 , United States
| | - Daniel L Cheney
- Molecular Structure and Design , Bristol-Myers Squibb Company , P.O. Box 5400, Princeton , New Jersey 08543 , United States
| | - 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 30332-0400 , United States
| |
Collapse
|
9
|
Hameed R, Khan A, van Mourik T. Intramolecular BSSE and dispersion affect the structure of a dipeptide conformer. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1418029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Rabia Hameed
- School of Chemistry, University of St Andrews, St Andrews, United Kingdom
| | - Afsar Khan
- Department of Chemistry, COMSATS Institute of Information Technology, Abbottabad, Pakistan
| | - Tanja van Mourik
- School of Chemistry, University of St Andrews, St Andrews, United Kingdom
| |
Collapse
|
10
|
Lee SJ, Miyamoto K, Ding F, Manby FR, Miller TF. Density-based errors in mixed-basis mean-field electronic structure, with implications for embedding and QM/MM methods. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.04.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
11
|
Jensen F. Using valence bond methods to estimate intramolecular basis set superposition errors. J Chem Phys 2017. [DOI: 10.1063/1.4983229] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
12
|
Affiliation(s)
- Balazs Nagy
- Department of Chemistry; Aarhus University; Aarhus Denmark
| | - Frank Jensen
- Department of Chemistry; Aarhus University; Aarhus Denmark
| |
Collapse
|
13
|
Baggioli A, Cavallotti CA, Famulari A. Exploring short intramolecular interactions in alkylaromatic substrates. Phys Chem Chem Phys 2016; 18:29616-29628. [PMID: 27753437 DOI: 10.1039/c6cp03323g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
From proteins and peptides to semiconducting polymers, aliphatic chains on aromatic groups are recurring motifs in macromolecules from very diverse application fields. Fields in which molecular folding and packing determine the macroscopic physical properties that make such advanced materials appealing in the first place. Within each macromolecule, the intrinsic structure of each unit defines how it interacts with its neighbours, ultimately opening up or denying certain backbone conformations. This eventually also determines how macromolecules interact with each other. This account deals specifically with the conformational problem of many common alkylaromatic units, examining the features of an intramolecular interaction involving a side chain with as few as three methylene groups. A set of 23 model compounds featuring an intramolecular interaction between an aliphatic X-H (X = C, N, O, and S) bond and an aromatic ring was considered. Quantitative computational analysis was made possible, thanks to complete basis set extrapolated CCSD(T) calculations and NCI topological analysis, the latter of which revealed an elaborate network of dispersive and steric interactions leading to somewhat unintuitive and unexpected results, such as the higher energetic stability of certain twisted conformational isomers over those with extended side chains. Vicinal covalent effects from polarizing groups and various heteroatoms, along with the occurrence of non-dispersive phenomena, were also investigated. The conclusions drawn from the investigation include a comprehensive set of guidelines intended to aid in the prediction of the most stable conformation for this class of building blocks. Our findings affect a variety of different research fields, including the tailoring of functional materials for organic electronics and photovoltaics, with insights into a rational treatment of conformational disorder, and the study of protein- and peptide-folding preferences, putting an emphasis on peculiar interactions between the backbone and aromatic residues.
Collapse
Affiliation(s)
- Alberto Baggioli
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
| | - Carlo A Cavallotti
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
| | - Antonino Famulari
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "G. Natta", Politecnico di Milano, via Mancinelli 7, I-20131 Milano, Italy.
| |
Collapse
|
14
|
Kulik HJ, Seelam N, Mar BD, Martínez TJ. Adapting DFT+U for the Chemically Motivated Correction of Minimal Basis Set Incompleteness. J Phys Chem A 2016; 120:5939-49. [DOI: 10.1021/acs.jpca.6b04527] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Heather J. Kulik
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 United States
| | - Natasha Seelam
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 United States
| | - Brendan D. Mar
- Department
of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 United States
| | - Todd J. Martínez
- Department
of Chemistry and PULSE Institute, Stanford University, Stanford, California 94305, United States
- SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| |
Collapse
|
15
|
Sure R, Brandenburg JG, Grimme S. Small Atomic Orbital Basis Set First-Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources. ChemistryOpen 2016; 5:94-109. [PMID: 27308221 PMCID: PMC4906470 DOI: 10.1002/open.201500192] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 11/12/2022] Open
Abstract
In quantum chemical computations the combination of Hartree-Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double-zeta quality is still widely used, for example, in the popular B3LYP/6-31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean-field methods.
Collapse
Affiliation(s)
- Rebecca Sure
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstr. 453115BonnGermany
| | - Jan Gerit Brandenburg
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstr. 453115BonnGermany
| | - Stefan Grimme
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstr. 453115BonnGermany
| |
Collapse
|
16
|
Cheng X, Herr JD, Steele RP. Accelerating Ab Initio Path Integral Simulations via Imaginary Multiple-Timestepping. J Chem Theory Comput 2016; 12:1627-38. [DOI: 10.1021/acs.jctc.6b00021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiaolu Cheng
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Jonathan D. Herr
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - Ryan P. Steele
- Department of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| |
Collapse
|
17
|
Jensen F. An Atomic Counterpoise Method for Estimating Inter- and Intramolecular Basis Set Superposition Errors. J Chem Theory Comput 2015; 6:100-6. [PMID: 26614323 DOI: 10.1021/ct900436f] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An atomic counterpoise method is proposed to calculate estimates of inter- and intramolecular basis set superposition errors. The method estimates the basis set superposition error as a sum of atomic contributions and can be applied for both independent particle and electron correlation models. It is shown that the atomic counterpoise method provides results very similar to the molecular counterpoise method for intermolecular basis set superposition errors at both the HF and MP2 levels of theory with a sequence of increasingly larger basis sets. The advantage of the atomic counterpoise method is that it can be applied with equal ease to estimate intramolecular basis set superposition errors, for which few other methods exist. The atomic counterpoise method is computationally quite efficient, requiring typically double the amount of computer time as required for calculating the uncorrected energy.
Collapse
Affiliation(s)
- Frank Jensen
- Department of Chemistry, University of Aarhus Langelandsgade 140, DK-8000 Aarhus, Denmark
| |
Collapse
|
18
|
Steele RP. Multiple-Timestep ab Initio Molecular Dynamics Using an Atomic Basis Set Partitioning. J Phys Chem A 2015; 119:12119-30. [DOI: 10.1021/acs.jpca.5b05850] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ryan P. Steele
- Department of Chemistry and
Henry Eyring Center for Theoretical Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| |
Collapse
|
19
|
Yang B, Wu RR, Rodgers MT. Base-Pairing Energies of Proton-Bound Dimers and Proton Affinities of 1-Methyl-5-Halocytosines: Implications for the Effects of Halogenation on the Stability of the DNA i-Motif. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1469-1482. [PMID: 26148525 DOI: 10.1007/s13361-015-1174-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Revised: 04/22/2015] [Accepted: 04/24/2015] [Indexed: 06/04/2023]
Abstract
(CCG)(n)•(CGG)(n) trinucleotide repeats have been found to be associated with fragile X syndrome, the most widespread inherited cause of mental retardation in humans. The (CCG)(n)•(CGG)(n) repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of noncanonical proton-bound dimers of cytosine (C(+)•C). Halogenated cytosine residues are one form of DNA damage that may be important in altering the structure and stability of DNA or DNA-protein interactions and, hence, regulate gene expression. Previously, we investigated the effects of 5-halogenation and 1-methylation of cytosine on the base-pairing energies (BPEs) using threshold collision-induced dissociation (TCID) techniques. In the present study, we extend our work to include proton-bound homo- and heterodimers of cytosine, 1-methyl-5-fluorocytosine, and 1-methyl-5-bromocytosine. All modifications examined here are found to produce a decrease in the BPEs. However, the BPEs of all of the proton-bound dimers examined significantly exceed those of Watson-Crick G•C, neutral C•C base pairs, and various methylated variants such that DNA i-motif conformations should still be preserved in the presence of these modifications. The proton affinities (PAs) of the halogenated cytosines are also obtained from the experimental data by competitive analysis of the primary dissociation pathways that occur in parallel for the proton-bound heterodimers. 5-Halogenation leads to a decrease in the N3 PA of cytosine, whereas 1-methylation leads to an increase in the N3 PA. Thus, the 1-methyl-5-halocytosines exhibit PAs that are intermediate.
Collapse
Affiliation(s)
- Bo Yang
- Department of Chemistry, Wayne State University, Detroit, MI, 48202, USA
| | | | | |
Collapse
|
20
|
Holroyd LF, van Mourik T. Tyrosine-glycine revisited: Resolving the discrepancy between theory and experiment. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.12.055] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
21
|
Yang B, Moehlig AR, Frieler CE, Rodgers MT. Base-pairing energies of protonated nucleobase pairs and proton affinities of 1-methylated cytosines: model systems for the effects of the sugar moiety on the stability of DNA i-motif conformations. J Phys Chem B 2015; 119:1857-68. [PMID: 25565341 DOI: 10.1021/acs.jpcb.5b00035] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Expansion of (CCG)n·(CGG)n trinucleotide repeats leads to hypermethylation of cytosine residues and results in Fragile X syndrome, the most common cause of inherited intellectual disability in humans. The (CCG)n·(CGG)n repeats adopt i-motif conformations that are preferentially stabilized by base-pairing interactions of noncanonical protonated nucleobase pairs of cytosine (C(+)·C). Previously, we investigated the effects of 5-methylation of cytosine on the base-pairing energies (BPEs) using threshold collision-induced dissociation (TCID) techniques. In the present work, we extend our investigations to include protonated homo- and heteronucleobase pairs of cytosine, 1-methylcytosine, 5-methylcytosine, and 1,5-dimethylcytosine. The 1-methyl substituent prevents most tautomerization processes of cytosine and serves as a mimic for the sugar moiety of DNA nucleotides. In contrast to permethylation of cytosine at the 5-position, 1-methylation is found to exert very little influence on the BPE. All modifications to both nucleobases lead to a small increase in the BPEs, with 5-methylation producing a larger enhancement than either 1-methyl or 1,5-dimethylation. In contrast, modifications to a single nucleobase are found to produce a small decrease in the BPEs, again with 5-methylation producing a larger effect than 1-methylation. However, the BPEs of all of the protonated nucleobase pairs examined here significantly exceed those of canonical G·C and neutral C·C base pairs, and thus should still provide the driving force stabilizing DNA i-motif conformations even in the presence of such modifications. The proton affinities of the methylated cytosines are also obtained from the TCID experiments by competitive analyses of the primary dissociation pathways that occur in parallel for the protonated heteronucleobase pairs.
Collapse
Affiliation(s)
- Bo Yang
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | | | | | | |
Collapse
|
22
|
Goerigk L, Collyer CA, Reimers JR. Recommending Hartree–Fock Theory with London-Dispersion and Basis-Set-Superposition Corrections for the Optimization or Quantum Refinement of Protein Structures. J Phys Chem B 2014; 118:14612-26. [DOI: 10.1021/jp510148h] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Lars Goerigk
- School
of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Charles A. Collyer
- School
of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jeffrey R. Reimers
- Centre
for Quantum and Molecular Structure, College of Sciences, Shanghai University, Shanghai 200444, China
- School
of Physics and Advanced Materials, The University of Technology, Sydney, New South Wales 2007, Australia
| |
Collapse
|
23
|
DFT optimization and DFT-MD studies of glucose, ten explicit water molecules enclosed by an implicit solvent, COSMO. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2013.12.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
24
|
Yang B, Rodgers MT. Base-pairing energies of proton-bound heterodimers of cytosine and modified cytosines: implications for the stability of DNA i-motif conformations. J Am Chem Soc 2013; 136:282-90. [PMID: 24320604 DOI: 10.1021/ja409515v] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The DNA i-motif conformation was discovered in (CCG)•(CGG)n trinucleotide repeats, which are associated with fragile X syndrome, the most widespread inherited cause of mental retardation in humans. The DNA i-motif is a four-stranded structure whose strands are held together by proton-bound dimers of cytosine (C(+)•C). The stronger base-pairing interactions in C(+)•C proton-bound dimers as compared to Watson-Crick G•C base pairs are the major forces responsible for stabilization of i-motif conformations. Methylation of cytosine results in silencing of the FMR1 gene and causes fragile X syndrome. However, the influence of methylation or other modifications such as halogenation of cytosine on the base-pairing energies (BPEs) in the i-motif remains elusive. To address this, proton-bound heterodimers of cytosine and 5-methylcytosine, 5-fluorocytosine, 5-bromocytosine, and 5-iodocytosine are probed in detail. Experimentally, the BPEs of proton-bound heterodimers of cytosine and modified cytosines are determined using threshold collision-induced dissociation (TCID) techniques. All modifications at the 5-position of cytosine are found to lower the BPE and therefore would tend to destabilize DNA i-motif conformations. However, the BPEs in these proton-bound heterodimers still significantly exceed those of the Watson-Crick G•C and neutral C•C base pairs, suggesting that C(+)•C mismatches are still energetically favored such that i-motif conformations are preserved. Excellent agreement between TCID measured BPEs and B3LYP calculated values is found with the def2-TZVPPD and 6-311+G(2d,2p) basis sets, suggesting that calculations at these levels of theory can be employed to provide reliable energetic predictions for related systems.
Collapse
Affiliation(s)
- Bo Yang
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | | |
Collapse
|
25
|
Vacek Chocholoušová J, Vacek J, Andronova A, Míšek J, Songis O, Šámal M, Stará IG, Meyer M, Bourdillon M, Pospíšil L, Starý I. On the Physicochemical Properties of Pyridohelicenes. Chemistry 2013; 20:877-93. [DOI: 10.1002/chem.201204410] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 10/04/2013] [Indexed: 11/08/2022]
|
26
|
Navrátil V, Klusák V, Rulíšek L. Theoretical Aspects of Hydrolysis of Peptide Bonds by Zinc Metalloenzymes. Chemistry 2013; 19:16634-45. [DOI: 10.1002/chem.201302663] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 08/08/2013] [Indexed: 12/11/2022]
Affiliation(s)
- Václav Navrátil
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences & IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Praha 6 (Czech Republic)
- Charles University in Prague, Faculty of Science, Department of Biochemistry, Hlavova 2030, 128 43 Praha 2 (Czech Republic)
| | - Vojtěch Klusák
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences & IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Praha 6 (Czech Republic)
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences & IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Praha 6 (Czech Republic)
| |
Collapse
|
27
|
Yang B, Wu RR, Rodgers MT. Base-pairing energies of proton-bound homodimers determined by guided ion beam tandem mass spectrometry: application to cytosine and 5-substituted cytosines. Anal Chem 2013; 85:11000-6. [PMID: 24117448 DOI: 10.1021/ac402542g] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Base-pairing interactions in proton-bound dimers of cytosine (C(+)·C) are the major forces responsible for stabilization of DNA i-motif conformations. Permethylation of cytosine in extended (CCG)·(CGG)n trinucleotide repeats has been shown to cause fragile-X syndrome, the most widespread inherited cause of mental retardation in humans. Oligonucleotides containing 5-bromo- or 5-fluorocytosine can bind to proteins that selectively bind methylated DNA, suggesting that halogenated cytosine damage products can potentially mimic methylation signals. However, the influence of methylation or halogenation on the base-pairing energies (BPEs) of proton-bound dimers of cytosine and their impact on the stability of DNA i-motif conformations is presently unknown. To address this, proton-bound homodimers of cytosine and 5-methyl-, 5-fluoro-, 5-bromo-, and 5-iodocytosine are investigated in detail both experimentally and theoretically. The BPEs of proton-bound homodimers of cytosine and the modified cytosines are measured by threshold collision-induced dissociation (TCID) techniques. 5-Methylation of cytosine is found to increase the BPE and would therefore tend to stabilize DNA i-motif conformations. In contrast, 5-halogenation lowers the BPE. However, the BPEs of the proton-bound 5-halocytosine homodimers examined here still significantly exceed that of Watson-Crick G·C base pairs, such that DNA i-motif conformations should be preserved in the presence of these modifications. Excellent agreement between TCID measured and B3LYP calculated BPEs is found, suggesting that B3LYP calculations can be used to provide reliable energetic predictions for related systems.
Collapse
Affiliation(s)
- Bo Yang
- Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States
| | | | | |
Collapse
|
28
|
Goerigk L, Reimers JR. Efficient Methods for the Quantum Chemical Treatment of Protein Structures: The Effects of London-Dispersion and Basis-Set Incompleteness on Peptide and Water-Cluster Geometries. J Chem Theory Comput 2013; 9:3240-51. [DOI: 10.1021/ct400321m] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Lars Goerigk
- School of Chemistry, The University of Sydney, New South Wales 2006, Australia
| | - Jeffrey R. Reimers
- School of Chemistry, The University of Sydney, New South Wales 2006, Australia
| |
Collapse
|
29
|
Nakai Y, Mori T, Sato K, Inoue Y. Theoretical and Experimental Studies of Circular Dichroism of Mono- and Diazonia[6]helicenes. J Phys Chem A 2013; 117:5082-92. [DOI: 10.1021/jp403426w] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Yoshito Nakai
- Department of Applied
Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871,
Japan
| | - Tadashi Mori
- Department of Applied
Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871,
Japan
| | - Kiyoshi Sato
- Division of Applied
Chemistry,
Faculty of Urban Environmental Sciences, Tokyo Metropolitan University, 1-1 minami-ohsawa, Hachioji, Tokyo 192-0397,
Japan
| | - Yoshihisa Inoue
- Department of Applied
Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871,
Japan
| |
Collapse
|
30
|
Strutyński K, Melle-Franco M, Gomes JANF. New parameterization scheme of DFT-D for graphitic materials. J Phys Chem A 2013; 117:2844-53. [PMID: 23473398 DOI: 10.1021/jp312239n] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new parametrization scheme of DFT-D is proposed with the aim of devising a methodology for the study of graphitic material. The main feature of the new system is the geometry optimization within the fitting scheme. The DFT-D parameters are obtained for the benzene dimer, a good model molecule for graphitic systems. Very accurate CCSD(T) results are used as reference data for the benzene dimer, and the new method is shown to reproduce accurately its binding energies with small basis sets. After geometry optimization our new scheme performs better than the other methods. This approach generates proper geometries and accurate binding energies, even with small basis sets. We can expect this method to give similarly good results for larger graphitic systems.
Collapse
Affiliation(s)
- Karol Strutyński
- REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre S/N, 4169-007 Porto, Portugal
| | | | | |
Collapse
|
31
|
Boonyarattanakalin S, Ruchirawat S, Gleeson MP. Ring opening polymerization of mannosyl tricyclic orthoesters: rationalising the stereo and regioselectivity of glycosidic bond formation using quantum chemical calculations. MEDCHEMCOMM 2013. [DOI: 10.1039/c2md20178j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantum chemical methods have been used to assess the physico-chemical origin of the stereo and regio-selectivity during glycosyl tricyclic orthoester polymerization. The subtle modulation of steric and electronic factors dramatically influences the reaction.
Collapse
Affiliation(s)
- Siwarutt Boonyarattanakalin
- School of Bio-Chemical Engineering and Technology
- Sirindhorn International Institute of Technology
- Thammasat University
- Thailand
| | - Somsak Ruchirawat
- Laboratory of Medicinal Chemistry
- Chulabhorn Research Institute
- Bangkok 10210
- Thailand
- Chemical Biology Program
| | - M. Paul Gleeson
- Department of Chemistry
- Faculty of Science
- Kasetsart University
- Bangkok 10900
- Thailand
| |
Collapse
|
32
|
Nakai Y, Mori T, Inoue Y. Circular Dichroism of (Di)methyl- and Diaza[6]helicenes. A Combined Theoretical and Experimental Study. J Phys Chem A 2012. [DOI: 10.1021/jp3104084] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yoshito Nakai
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871,
Japan
| | - Tadashi Mori
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871,
Japan
| | - Yoshihisa Inoue
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871,
Japan
| |
Collapse
|
33
|
Kruse H, Goerigk L, Grimme S. Why the Standard B3LYP/6-31G* Model Chemistry Should Not Be Used in DFT Calculations of Molecular Thermochemistry: Understanding and Correcting the Problem. J Org Chem 2012; 77:10824-34. [DOI: 10.1021/jo302156p] [Citation(s) in RCA: 320] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Holger Kruse
- Theoretische Organische Chemie, Organisch-Chemisches Institut der Universität Münster, Corrensstrasse 40, D-48149 Münster, Germany
| | - Lars Goerigk
- School of Chemistry, The University of Sydney, Sydney, New South Wales 2006,
Australia
| | - Stefan Grimme
- Mulliken Center
for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstrasse 4,
D-53115 Bonn, Germany
| |
Collapse
|
34
|
Šponer J, Mládek A, Šponer JE, Svozil D, Zgarbová M, Banáš P, Jurečka P, Otyepka M. The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies. Phys Chem Chem Phys 2012; 14:15257-77. [PMID: 23072945 DOI: 10.1039/c2cp41987d] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Knowledge of geometrical and physico-chemical properties of the sugar-phosphate backbone substantially contributes to the comprehension of the structural dynamics, function and evolution of nucleic acids. We provide a side by side overview of structural biology/bioinformatics, quantum chemical and molecular mechanical/simulation studies of the nucleic acids backbone. We highlight main features, advantages and limitations of these techniques, with a special emphasis given to their synergy. The present status of the research is then illustrated by selected examples which include classification of DNA and RNA backbone families, benchmark structure-energy quantum chemical calculations, parameterization of the dihedral space of simulation force fields, incorporation of arsenate into DNA, sugar-phosphate backbone self-cleavage in small RNA enzymes, and intricate geometries of the backbone in recurrent RNA building blocks. Although not apparent from the current literature showing limited overlaps between the QM, simulation and bioinformatics studies of the nucleic acids backbone, there in fact should be a major cooperative interaction between these three approaches in studies of the sugar-phosphate backbone.
Collapse
Affiliation(s)
- Jiří Šponer
- Institute of Biophysics, Academy Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic.
| | | | | | | | | | | | | | | |
Collapse
|
35
|
Assessment of density functionals on intramolecular dispersion interaction in large normal alkanes. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.05.067] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
36
|
Nakai Y, Mori T, Inoue Y. Theoretical and Experimental Studies on Circular Dichroism of Carbo[n]helicenes. J Phys Chem A 2012; 116:7372-85. [DOI: 10.1021/jp304576g] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Yoshito Nakai
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871,
Japan
| | - Tadashi Mori
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871,
Japan
| | - Yoshihisa Inoue
- Department
of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita, Osaka 565-0871,
Japan
| |
Collapse
|
37
|
Kruse H, Grimme S. A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems. J Chem Phys 2012; 136:154101. [DOI: 10.1063/1.3700154] [Citation(s) in RCA: 414] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
38
|
Rokob TA, Srnec M, Rulíšek L. Theoretical calculations of physico-chemical and spectroscopic properties of bioinorganic systems: current limits and perspectives. Dalton Trans 2012; 41:5754-68. [DOI: 10.1039/c2dt12423h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
39
|
Affiliation(s)
- Yun Shen
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- Graduate School, Chinese Academy of Sciences, Beijing 100049, China
| | - Chuan-Feng Chen
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| |
Collapse
|
40
|
Zgarbová M, Otyepka M, Šponer J, Mládek A, Banáš P, Cheatham TE, Jurečka P. Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles. J Chem Theory Comput 2011; 7:2886-2902. [PMID: 21921995 PMCID: PMC3171997 DOI: 10.1021/ct200162x] [Citation(s) in RCA: 771] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Indexed: 01/19/2023]
Abstract
We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force field for RNA, χ(OL). The parameters remove destabilization of the anti region found in the ff99 force field and thus prevent formation of spurious ladder-like structural distortions in RNA simulations. They also improve the description of the syn region and the syn-anti balance as well as enhance MD simulations of various RNA structures. Although χ(OL) can be combined with both ff99 and ff99bsc0, we recommend the latter. We do not recommend using χ(OL) for B-DNA because it does not improve upon ff99bsc0 for canonical structures. However, it might be useful in simulations of DNA molecules containing syn nucleotides. Our parametrization is based on high-level QM calculations and differs from conventional parametrization approaches in that it incorporates some previously neglected solvation-related effects (which appear to be essential for obtaining correct anti/high-anti balance). Our χ(OL) force field is compared with several previous glycosidic torsion parametrizations.
Collapse
Affiliation(s)
- Marie Zgarbová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 77146 Olomouc, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 77146 Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jiří Šponer
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 77146 Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Arnošt Mládek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 77146 Olomouc, Czech Republic
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Thomas E. Cheatham
- Departments of Medicinal Chemistry and Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 2000 East 30 South Skaggs 201, Salt Lake City, Utah 84112, United States
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 17 listopadu 12, 77146 Olomouc, Czech Republic
| |
Collapse
|
41
|
Hua S, Xu L, Li W, Li S. Cooperativity in Long α- and 310-Helical Polyalanines: Both Electrostatic and van der Waals Interactions Are Essential. J Phys Chem B 2011; 115:11462-9. [DOI: 10.1021/jp203423w] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shugui Hua
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Lina Xu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of MOE, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, P. R. China
| |
Collapse
|
42
|
Balabin RM. Enthalpy difference between conformations of normal alkanes: effects of basis set and chain length on intramolecular basis set superposition error. Mol Phys 2011. [DOI: 10.1080/00268976.2011.558858] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
43
|
Riley KE, Hobza P. Noncovalent interactions in biochemistry. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.8] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kevin E. Riley
- Department of Chemistry, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague, Czech Republic
- Department of Physical Chemistry, Palacky University, Olomouc, Czech Republic
| |
Collapse
|
44
|
Lagutschenkov A, Langer J, Berden G, Oomens J, Dopfer O. Infrared spectra of protonated neurotransmitters: dopamine. Phys Chem Chem Phys 2011; 13:2815-23. [DOI: 10.1039/c0cp02133d] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
45
|
Riley KE, Pitonák M, Jurecka P, Hobza P. Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories. Chem Rev 2010; 110:5023-63. [PMID: 20486691 DOI: 10.1021/cr1000173] [Citation(s) in RCA: 570] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kevin E Riley
- Department of Chemistry, University of Puerto Rico, Rio Piedras, Puerto Rico 00931
| | | | | | | |
Collapse
|
46
|
Mládek A, Šponer JE, Jurečka P, Banáš P, Otyepka M, Svozil D, Šponer J. Conformational Energies of DNA Sugar−Phosphate Backbone: Reference QM Calculations and a Comparison with Density Functional Theory and Molecular Mechanics. J Chem Theory Comput 2010. [DOI: 10.1021/ct1004593] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Arnošt Mládek
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 771 46 Olomouc, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology, Technická 3, 166 28 Prague 6, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6,
| | - Judit E. Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 771 46 Olomouc, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology, Technická 3, 166 28 Prague 6, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6,
| | - Petr Jurečka
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 771 46 Olomouc, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology, Technická 3, 166 28 Prague 6, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6,
| | - Pavel Banáš
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 771 46 Olomouc, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology, Technická 3, 166 28 Prague 6, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6,
| | - Michal Otyepka
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 771 46 Olomouc, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology, Technická 3, 166 28 Prague 6, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6,
| | - Daniel Svozil
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 771 46 Olomouc, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology, Technická 3, 166 28 Prague 6, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6,
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Physical Chemistry, Faculty of Science, Palacký University, 771 46 Olomouc, Czech Republic, Laboratory of Informatics and Chemistry, Faculty of Chemical Technology, Institute of Chemical Technology, Technická 3, 166 28 Prague 6, Czech Republic, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6,
| |
Collapse
|
47
|
Zhang IY, Luo Y, Xu X. Basis set dependence of the doubly hybrid XYG3 functional. J Chem Phys 2010; 133:104105. [DOI: 10.1063/1.3488649] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
|
48
|
Bretherick NH, van Mourik T. π Interactions Studied with Electronic Structure Methods: The Ethyne Methyl Isocyanide Complex and Thioanisole. J Chem Theory Comput 2010; 6:2687-700. [DOI: 10.1021/ct100295f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Natalie H. Bretherick
- School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, United Kingdom
| | - Tanja van Mourik
- School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife, KY16 9ST, Scotland, United Kingdom
| |
Collapse
|
49
|
Indarto A, Giordana A, Ghigo G, Maranzana A, Tonachini G. Polycyclic aromatic hydrocarbon formation mechanism in the “particle phase”. A theoretical study. Phys Chem Chem Phys 2010; 12:9429-40. [DOI: 10.1039/c000491j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
50
|
Johansson M, Patzschke M. Fixing the Chirality and Trapping the Transition State of Helicene with Atomic Metal Glue. Chemistry 2009; 15:13210-8. [DOI: 10.1002/chem.200901656] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|