1
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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.
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Affiliation(s)
- Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus, Denmark
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2
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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.
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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
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3
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Pedersen J, Mikkelsen KV. A benchmark study of aromaticity indexes for benzene, pyridine and the diazines - I. Ground state aromaticity. RSC Adv 2022; 12:2830-2842. [PMID: 35425306 PMCID: PMC8979194 DOI: 10.1039/d2ra00093h] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 01/07/2022] [Indexed: 11/21/2022] Open
Abstract
Five different aromaticity indexes are benchmarked for benzene, pyridine and the diazines in their ground states. A basis set study was performed using the Pople style, Karlsruhe and Dunning's correlation consistent basis sets. Ten different DFT functionals, including LSDA, PBE, PBE0, B3LYP, CAM-B3LYP, wB97XD, M06-2X, SOGGA11X, M11 and MN15 were benchmarked by comparison with CCSD, CASSCF and MP2. Large out-of-plane imaginary frequencies were observed for some of the optimized structures at the correlated wavefunction level of theory. It was found that the DFT functionals in general predict the para-delocalization index, multicenter index and aromatic fluctuation index to be approximately 70%, 50% and 45% larger, respectively, compared to the CCSD method. Comparisons of the DFT functionals showed that the wB97XD, CAM-B3LYP and M06-2X functionals performed the best. Furthermore, the basis set dependence of the DFT functionals was found to be large for the electron sharing indexes. Based on these findings, it is recommended to perform ground state calculations of aromaticity indexes at the wB97XD, CAM-B3LYP or M06-2X level of theory utilizing a simple basis set of triple-ζ quality. Five different aromaticity indexes are benchmarked for benzene, pyridine and the diazines in their ground states.![]()
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Affiliation(s)
- Jacob Pedersen
- Department of Chemistry, University of Copenhagen Copenhagen DK-2100 Denmark
| | - Kurt V Mikkelsen
- Department of Chemistry, University of Copenhagen Copenhagen DK-2100 Denmark
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4
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Lebedev AV. Pyridine and Methylpyridines: Calculations of the Structure, Proton Affinity, Gas-Phase Basicity, and Mobility of Protonated Molecules and Proton-Bound Dimers. JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1134/s1061934820130079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Abstract
Squaraine dyes are known for their particular optical properties. They exhibit intense photochemically stable fluorescence in usually (near) infra red region that can be quenched by intermolecular interactions. Moreover, even the centrosymmetric dyes feature non-zero second harmonic generation upon aggregation. Therefore, the detailed knowledge of the squaraine dye interaction nature both in homogenic aggregates and with other species present in the environment can be of importance for the design of new materials of desired properties. In the present study, interaction in squaraine dimers is investigated with quantum chemistry tools. Four structures: two stacked and two hydrogen-bonded are analyzed in terms of supermolecular approach and symmetry-adapted perturbation theory. MP2C/aug-cc-pVTZ supermolecular calculations confirm the particular stability of the stacked dimers and the favoured dispersion attraction for the long-displaced system.
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6
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Gloaguen E, Mons M, Schwing K, Gerhards M. Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues. Chem Rev 2020; 120:12490-12562. [PMID: 33152238 DOI: 10.1021/acs.chemrev.0c00168] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.
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Affiliation(s)
- Eric Gloaguen
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Kirsten Schwing
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - Markus Gerhards
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
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7
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A computational study of TyrGly hydration. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.113011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Abstract
Since the introduction of the fragment molecular orbital method 20 years ago, fragment-based approaches have occupied a small but growing niche in quantum chemistry. These methods decompose a large molecular system into subsystems small enough to be amenable to electronic structure calculations, following which the subsystem information is reassembled in order to approximate an otherwise intractable supersystem calculation. Fragmentation sidesteps the steep rise (with respect to system size) in the cost of ab initio calculations, replacing it with a distributed cost across numerous computer processors. Such methods are attractive, in part, because they are easily parallelizable and therefore readily amenable to exascale computing. As such, there has been hope that distributed computing might offer the proverbial "free lunch" in quantum chemistry, with the entrée being high-level calculations on very large systems. While fragment-based quantum chemistry can count many success stories, there also exists a seedy underbelly of rarely acknowledged problems. As these methods begin to mature, it is time to have a serious conversation about what they can and cannot be expected to accomplish in the near future. Both successes and challenges are highlighted in this Perspective.
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Affiliation(s)
- John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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9
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Alcolea Palafox M. Effect of the sulfur atom on S2 and S4 positions of the uracil ring in different DNA:RNA hybrid microhelixes with three nucleotide base pairs. Biopolymers 2019; 110:e23247. [PMID: 30676643 DOI: 10.1002/bip.23247] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 11/03/2018] [Accepted: 11/07/2018] [Indexed: 02/06/2023]
Abstract
The effect of the sulphur atom on the uracil ring was analyzed in different DNA:RNA microhelixes with three nucleotide base-pairs, including uridine, 2-thiouridine, 4-thiouridine, 2,4-dithiouridine, cytidine, adenosine and guanosine. Distinct backbone and helical parameters were optimized at different density functional (DFT) levels. The Watson-Crick pair with 2-thiouridine appears weaker than with uridine, but its interaction with water molecules appears easier. Two types of microhelixes were found, depending on the H-bond of H2' hydroxyl atom: A-type appears with the ribose ring in 3 E-envelope C3' -endo, and B-type in 2 E-envelope C2' -endo. B-type is less common but it is more stable and with higher dipole-moment. The sulphur atoms significantly increase the dipole-moment of the microhelix, as well as the rise and propeller twist parameters. Simulations with four Na atoms H-bonded to the phosphate groups, and further hydration with explicit water molecules were carried out. A re-definition of the numerical value calculation of several base-pair and base-stacking parameters is suggested.
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Affiliation(s)
- Mauricio Alcolea Palafox
- Departamento de Química-Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain
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10
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El Guerdaoui A, Tijar R, Bourjila M, El Merbouh B, El Bouzaidi RD, El Gridani A. Conformational Space Analysis of Protected N-Formyl-L-Phenylalanine-N-Amide Amino Acid: Effects of the Intramolecular Basis Set Superposition Error. J STRUCT CHEM+ 2019. [DOI: 10.1134/s0022476619010049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Comparative conformational studies of 3,4,6-tri- O -acetyl-1,5-anhydro-2-deoxyhex-1-enitols at the DFT level. Carbohydr Res 2018; 462:13-27. [DOI: 10.1016/j.carres.2018.03.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 03/20/2018] [Accepted: 03/25/2018] [Indexed: 11/24/2022]
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12
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Li J, Xu T, Ping Y, van Mourik T, Früchtl H, Kirk SR, Jenkins S. Consequences of theory level choice evaluated with new tools from QTAIM and the stress tensor for a dipeptide conformer. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.02.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Chen N, Zhang F, Wu R, Hess BA. Biosynthesis of Spinosyn A: A [4 + 2] or [6 + 4] Cycloaddition? ACS Catal 2018. [DOI: 10.1021/acscatal.7b03908] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Nanhao Chen
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
- Department
of Chemistry, University of California, Davis, California 95616, United States
| | - Fan Zhang
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Ruibo Wu
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - B. Andes Hess
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
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14
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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
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15
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McDonagh JL, Silva AF, Vincent MA, Popelier PLA. Machine Learning of Dynamic Electron Correlation Energies from Topological Atoms. J Chem Theory Comput 2017; 14:216-224. [PMID: 29211469 DOI: 10.1021/acs.jctc.7b01157] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We present an innovative method for predicting the dynamic electron correlation energy of an atom or a bond in a molecule utilizing topological atoms. Our approach uses the machine learning method Kriging (Gaussian Process Regression with a non-zero mean function) to predict these dynamic electron correlation energy contributions. The true energy values are calculated by partitioning the MP2 two-particle density-matrix via the Interacting Quantum Atoms (IQA) procedure. To our knowledge, this is the first time such energies have been predicted by a machine learning technique. We present here three important proof-of-concept cases: the water monomer, the water dimer, and the van der Waals complex H2···He. These cases represent the final step toward the design of a full IQA potential for molecular simulation. This final piece will enable us to consider situations in which dispersion is the dominant intermolecular interaction. The results from these examples suggest a new method by which dispersion potentials for molecular simulation can be generated.
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Affiliation(s)
- James L McDonagh
- Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, Great Britain
| | - Arnaldo F Silva
- Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, Great Britain
| | - Mark A Vincent
- School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, Great Britain
| | - Paul L A Popelier
- Manchester Institute of Biotechnology, The University of Manchester , 131 Princess Street, Manchester M1 7DN, Great Britain.,School of Chemistry, The University of Manchester , Oxford Road, Manchester M13 9PL, Great Britain
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16
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Smith DA, Holroyd LF, van Mourik T, Jones AC. A DFT study of 2-aminopurine-containing dinucleotides: prediction of stacked conformations with B-DNA structure. Phys Chem Chem Phys 2017; 18:14691-700. [PMID: 27186599 DOI: 10.1039/c5cp07816d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The fluorescence properties of dinucleotides incorporating 2-aminopurine (2AP) suggest that the simplest oligonucleotides adopt conformations similar to those found in duplex DNA. However, there is a lack of structural data for these systems. We report a density functional theory (DFT) study of the structures of 2AP-containing dinucleotides (deoxydinucleoside monophosphates), including full geometry optimisation of the sugar-phosphate backbone. Our DFT calculations employ the M06-2X functional for reliable treatment of dispersion interactions and include implicit aqueous solvation. Dinucleotides with 2AP in the 5'-position and each of the natural bases in the 3'-position are examined, together with the analogous 5'-adenine-containing systems. Computed structures are compared in detail with typical B-DNA base-step parameters, backbone torsional angles and sugar pucker, derived from crystallographic data. We find that 2AP-containing dinucleotides adopt structures that closely conform to B-DNA in all characteristic parameters. The structures of 2AP-containing dinucleotides closely resemble those of their adenine-containing counterparts, demonstrating the fidelity of 2AP as a mimic of the natural base. As a first step towards exploring the conformational heterogeneity of dinucleotides, we also characterise an imperfectly stacked conformation and one in which the bases are completely unstacked.
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Affiliation(s)
- Darren A Smith
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
| | - Leo F Holroyd
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK
| | - Anita C Jones
- EaStCHEM School of Chemistry, The University of Edinburgh, David Brewster Road, Edinburgh, EH9 3FJ, UK.
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17
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Affiliation(s)
- Balazs Nagy
- Department of Chemistry; Aarhus University; Aarhus Denmark
| | - Frank Jensen
- Department of Chemistry; Aarhus University; Aarhus Denmark
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18
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Møller KH, Otkjær RV, Hyttinen N, Kurtén T, Kjaergaard HG. Cost-Effective Implementation of Multiconformer Transition State Theory for Peroxy Radical Hydrogen Shift Reactions. J Phys Chem A 2016; 120:10072-10087. [DOI: 10.1021/acs.jpca.6b09370] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Kristian H. Møller
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Rasmus V. Otkjær
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Noora Hyttinen
- Department
of Chemistry, University of Helsinki, POB 55, FIN-00014 Helsinki, Finland
| | - Theo Kurtén
- Department
of Chemistry, University of Helsinki, POB 55, FIN-00014 Helsinki, Finland
| | - Henrik G. Kjaergaard
- Department
of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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19
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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.
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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.
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20
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McDonagh JL, Vincent MA, Popelier PL. Partitioning dynamic electron correlation energy: Viewing Møller-Plesset correlation energies through Interacting Quantum Atom (IQA) energy partitioning. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.09.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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Molecular aspects of squaraine dyes aggregation and its influence on spectroscopic properties. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1971-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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22
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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
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23
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Kumar NVS. A DFT study on the role of long range correlation interaction and solvent effects in homochiral and heterochiral cyclic trimerization of imidazole based heterocyclic amino acids. J Mol Model 2016; 22:141. [PMID: 27221744 DOI: 10.1007/s00894-016-3003-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/25/2016] [Indexed: 01/20/2023]
Abstract
Using B3LYP and B97D functionals of density functional theory (DFT), homochiral and heterochiral cyclic trimerization of imidazole based heterocyclic amino acids are studied in gas phase and solvent phase, i. e., Acetonitrile. Both the functionals show that formation of homochiral cyclic tripeptide is thermodynamically and kinetically favorable over its heterochiral counterpart in gas phase. The functional, B97D, decreases the height of reaction barriers significantly compared to those predicted by the functional B3LYP. The reaction pathways explored using PCM implicit solvent model show reduced kinetic favorability for formation of the homochiral cyclic tripeptide over its heterochiral counterpart. The results are substantiated by structural aspects.
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Affiliation(s)
- N V Suresh Kumar
- Department of Physics, K L University, Green fields, Vaddeswaram, Guntur, 522502, India.
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24
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Assessing the performance of popular QM methods for calculation of conformational energies of trialanine. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.04.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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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.
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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
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Kaminský J, Jensen F. Conformational Interconversions of Amino Acid Derivatives. J Chem Theory Comput 2016; 12:694-705. [PMID: 26691979 DOI: 10.1021/acs.jctc.5b00911] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Exhaustive conformational interconversions including transition structure analyses of N-acetyl-l-glycine-N-methylamide as well as its alanine, serine, and cysteine analogues have been investigated at the MP2/6-31G** level, yielding a total of 142 transition states. Improved estimates of relative energies were obtained by separately extrapolating the Hartree-Fock and MP2 energies to the basis set limit and adding the difference between CCSD(T) and MP2 results with the cc-pVDZ basis set to the extrapolated MP2 results. The performance of eight empirical force fields (AMBER94, AMBER14SB, MM2, MM3, MMFFs, CHARMM22_CMAP, OPLS_2005, and AMOEBAPRO13) in reproducing ab initio energies of transition states was tested. Our results indicate that commonly used class I force fields employing a fixed partial charge model for the electrostatic interaction provide mean errors in the ∼10 kJ/mol range for energies of conformational transition states for amino acid conformers. Modern reparametrized versions, such as CHARMM22_CMAP, and polarizable force fields, such as AMOEBAPRO13, have slightly lower mean errors, but maximal errors are still in the 35 kJ/mol range. There are differences between the force fields in their ability for reproducing conformational transitions classified according to backbone/side-chain or regions in the Ramachandran angles, but the data set is likely too small to draw any general conclusions. Errors in conformational interconversion barriers by ∼10 kJ/mol suggest that the commonly used force field may bias certain types of transitions by several orders of magnitude in rate and thus lead to incorrect dynamics in simulations. It is therefore suggested that information for conformational transition states should be included in parametrizations of new force fields.
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Affiliation(s)
- Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 166 10 Prague, Czech Republic
| | - Frank Jensen
- Department of Chemistry, Aarhus University , Langelandsgade 140, DK-8000 Aarhus C, Denmark
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27
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Nazarski RB, Wałejko P, Witkowski S. Multi-conformer molecules in solutions: an NMR-based DFT/MP2 conformational study of two glucopyranosides of a vitamin E model compound. Org Biomol Chem 2016; 14:3142-58. [DOI: 10.1039/c5ob01865j] [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
Overall geometries of both glucosyl derivatives of PMC were found on the basis of their NMR spectra in CDCl3and relatedδH,C/nJHHIEF-PCM(UFF,CHCl3)/DFT calculational results.
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Affiliation(s)
- Ryszard B. Nazarski
- University of Łódź
- Faculty of Chemistry
- Department of Theoretical and Structural Chemistry
- 90-236 Łódź
- Poland
| | - Piotr Wałejko
- University of Białystok
- Institute of Chemistry
- 15-245 Białystok
- Poland
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28
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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.
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Affiliation(s)
- Frank Jensen
- Department of Chemistry, University of Aarhus Langelandsgade 140, DK-8000 Aarhus, Denmark
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29
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Møller KH, Hansen AS, Kjaergaard HG. Gas Phase Detection of the NH-P Hydrogen Bond and Importance of Secondary Interactions. J Phys Chem A 2015; 119:10988-98. [PMID: 26451467 DOI: 10.1021/acs.jpca.5b08358] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have observed the NH···P hydrogen bond in a gas phase complex. The bond is identified in the dimethylamine-trimethylphosphine complex by a red shift of the fundamental NH-stretching frequency observed using Fourier transform infrared spectroscopy (FT-IR). On the basis of the measured NH-stretching frequency red shifts, we find that P is a hydrogen bond acceptor atom similar in strength to S. Both are stronger acceptors than O and significantly weaker acceptors than N. The hydrogen bond angle, ∠NHP, is found to be very sensitive to the functional employed in density functional theory (DFT) optimizations of the complex and is a possible parameter to assess the quality of DFT functionals. Natural bonding orbital (NBO) energies and results from the topological methods atoms in molecules (AIM) and noncovalent interactions (NCI) indicate that the sensitivity is caused by the weakness of the hydrogen bond compared to secondary interactions. We find that B3LYP favors the hydrogen bond and M06-2X favors the secondary interactions leading to under- and overestimation, respectively, of the hydrogen bond angle relative to a DF-LCCSD(T)-F12a calculated angle. The remaining functionals tested, B3LYP-D3, B3LYP-D3BJ, CAM-B3LYP, and ωB97X-D, as well as MP2, show comparable contributions from the hydrogen bond and the secondary interactions and are close to DF-LCCSD(T)-F12a results.
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Affiliation(s)
- Kristian H Møller
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Anne S Hansen
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Henrik G Kjaergaard
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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30
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Abstract
This chapter examines the structural characterisation of isolated neutral amino-acids and peptides. After a presentation of the experimental and theoretical state-of-the-art in the field, a review of the major structures and shaping interactions is presented. Special focus is made on conformationally-resolved studies which enable one to go beyond simple structural characterisation; probing flexibility and excited-state photophysics are given as examples of promising future directions.
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31
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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]
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32
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Braga CB, Ducati LC, Rittner R. Experimental and theoretical evaluation on the conformational behavior of l-aspartic acid dimethyl ester and its N-acetylated derivative. RSC Adv 2015. [DOI: 10.1039/c4ra14480e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The AspOMe and AcAspOMe conformational preferences and their corresponding intramolecular interactions were studied through spectroscopic and theoretical methodologies.
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Affiliation(s)
- Carolyne B. Braga
- Physical Organic Chemistry Laboratory
- Chemistry Institute
- University of Campinas
- Campinas
- Brazil
| | | | - Roberto Rittner
- Physical Organic Chemistry Laboratory
- Chemistry Institute
- University of Campinas
- Campinas
- Brazil
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33
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Assignment of O–O and Mo=O Stretching Frequencies of Molybdenum/Tungsten Complexes Revisited. J CHEM-NY 2015. [DOI: 10.1155/2015/439270] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The assignment of peroxo stretching frequencies for Molybdenum and Tungsten complexes is studied by DFT and MP2 calculations. We found that M06 functional is unsuitable for assignment of Mo=O and O–O stretches in CpMo(η2-O2)OCH3and we found that MP2 and even the def2-TZVP do not give accurate order of asymmetric and symmetric Mo=O stretching. We recommend the M06L, which is a good compromise between speed and accuracy, for works involving these complexes. For a series of ten Molybdenum and Tungsten complexes studied we found that, for Mo/W=O stretching frequencies at M06L/def2-TZVP, after scaling, a small RMSD of 15 cm−1could be obtained. However peroxo stretching frequencies RMSD remains high at 40 cm−1after scaling. This could potentially point out the need for reassignment of experimental peroxo frequencies in some of the works cited in this report.
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34
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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
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35
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Zehnacker A. Chirality effects in gas-phase spectroscopy and photophysics of molecular and ionic complexes: contribution of low and room temperature studies. INT REV PHYS CHEM 2014. [DOI: 10.1080/0144235x.2014.911548] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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36
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Suresh Kumar NV, Singh H. Density functional theory based study on cis-trans isomerism of the amide bond in homodimers of β(2,3)- and β(3)-substituted homoproline. J Phys Chem A 2014; 118:2120-37. [PMID: 24559065 DOI: 10.1021/jp500187z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Preference for a cis/trans peptide bond between residues of dipeptides formed by substituted β(2,3) (I) and β(3) (II) homoproline is investigated using density functional theory (DFT). Potential energy surfaces for monomer and linear dimers are explored at the B3LYP/6-31G(d,p) level of theory. Minimum energy conformations of the dipeptides are optimized using B3LYP, PBE1PBE, B97D, and M06-2X functionals at the 6-31G(d,p) level of basis set in both the gas phase and solvent phase. The relative free energy difference between the selected conformations is marginal. Results obtained using the functionals M06-2X and B97D on dimers of I and II, respectively, agree with experimental results. The lowest energy conformations predicted by B97D/6-31G(d,p) and M06-2X/6-31G(d,p) levels of theory show greater relative MP2 correlation energy. Dipeptides of I with hydrophilic substituents show preference for a trans peptide bond. Support for cis/trans isomerism in dimers of I with hydrophobic substituents comes from potential energy surfaces and free energy data. Although dipeptides of II with hydrophilic substituents show preference for cis peptide bond, the dipeptides with hydrophobic substituent prefer trans bond.
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Affiliation(s)
- N V Suresh Kumar
- Department of Physics, K L University , Greenfields, Vaddeswaram, Guntur 522502, Andhra Pradesh, India
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37
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Jeschke S, Wiemhöfer HD, Mück-Lichtenfeld C. Computational study of structural properties of lithium cation complexes with carbamate-modified disiloxanes. Phys Chem Chem Phys 2014; 16:14236-43. [DOI: 10.1039/c4cp01837k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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39
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40
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Mirijanian DT, Mannige RV, Zuckermann RN, Whitelam S. Development and use of an atomistic CHARMM-based forcefield for peptoid simulation. J Comput Chem 2013; 35:360-70. [DOI: 10.1002/jcc.23478] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 10/06/2013] [Indexed: 01/31/2023]
Affiliation(s)
- Dina T. Mirijanian
- Molecular Foundry, Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley California 94720
| | - Ranjan V. Mannige
- Molecular Foundry, Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley California 94720
| | - Ronald N. Zuckermann
- Molecular Foundry, Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley California 94720
| | - Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory; 1 Cyclotron Road Berkeley California 94720
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41
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Kitagawa Y, Kawakami T, Yamanaka S, Okumura M. DFT and DFT-D studies on molecular structure of double-decker phthalocyaninato-terbium(III) complex. Mol Phys 2013. [DOI: 10.1080/00268976.2013.825341] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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42
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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
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43
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On the Relevance of Considering the Intermolecular Interactions on the Prediction of the Vibrational Spectra of Isopropylamine. J CHEM-NY 2013. [DOI: 10.1155/2013/682514] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The effects of implicitly considering the effects of hydrogen bonding on the molecular properties, such as vibrational frequencies, were inferred on the basis of DFT calculations. Several clusters of isopropylamine were assembled and theoretically characterized. The results showed that maximum H-bond cooperativity is achieved when the amine group acts simultaneously as donor and acceptor. The effect of H-bond cooperativity manifests itself in the relative cluster stability and on the structural and vibrational frequency predictions. Referring to the vibrational frequencies it was found that theNH2stretching and torsion vibrational modes are the most affected by the amine involvement in hydrogen bonding. Both stretching modes were found to be significantly redshifted relative to the monomer. TheNH2torsional mode, on the other hand, was found to be blueshifted up to 350 cm-1. Finally, the comparative study between the theory levels performed allows to conclude that the small 6-31G* basis set is able to stabilize weakC–H⋯Ninteractions as long as the new dispersion corrected DFT methods are considered. The impairments observed with conventional DFT methods for describing weak interactions may be overcome with the improvement of basis set, but the associated increase of computational costs may turn the calculations unfeasible.
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44
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Skelton AA, Fried JR. The insertion of gas molecules into polyhedral oligomeric silsesquioxane (POSS) cages: understanding the energy of insertion using quantum chemical calculations. Phys Chem Chem Phys 2013; 15:4341-54. [DOI: 10.1039/c3cp43738h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Goldey M, Dutoi A, Head-Gordon M. Attenuated second-order Møller–Plesset perturbation theory: performance within the aug-cc-pVTZ basis. Phys Chem Chem Phys 2013; 15:15869-75. [DOI: 10.1039/c3cp51826d] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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46
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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
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47
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Van Houteghem M, Verstraelen T, Ghysels A, Vanduyfhuys L, Waroquier M, Van Speybroeck V. Analysis of the basis set superposition error in molecular dynamics of hydrogen-bonded liquids: application to methanol. J Chem Phys 2012; 137:104506. [PMID: 22979873 DOI: 10.1063/1.4749929] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An efficient protocol is presented to compensate for the basis set superposition error (BSSE) in DFT molecular dynamics (MD) simulations using localized Gaussian basis sets. We propose a classical correction term that can be added a posteriori to account for BSSE. It is tested to what extension this term will improve radial distribution functions (RDFs). The proposed term is pairwise between certain atoms in different molecules and was calibrated by fitting reference BSSE data points computed with the counterpoise method. It is verified that the proposed exponential decaying functional form of the model is valid. This work focuses on hydrogen-bonded liquids, i.e., methanol, and more specific on the intermolecular hydrogen bond, but in principle the method is generally applicable on any type of interaction where BSSE is significant. We evaluated the relative importance of the Grimme-dispersion versus BSSE and found that they are of the same order of magnitude, but with an opposite sign. Upon introduction of the correction, the relevant RDFs, obtained from MD, have amplitudes equal to experiment.
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Affiliation(s)
- Marc Van Houteghem
- Center for Molecular Modeling, QCMM Alliance Ghent-Brussels, Ghent University, Technologiepark 903, B-9052 Zwijnaarde, Belgium
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48
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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]
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49
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Hunter RS, van Mourik T. DNA base stacking: The stacked uracil/uracil and thymine/thymine minima. J Comput Chem 2012; 33:2161-72. [DOI: 10.1002/jcc.23052] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 06/01/2012] [Accepted: 06/04/2012] [Indexed: 01/24/2023]
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50
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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
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