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Stylianakis I, Zervos N, Lii JH, Pantazis DA, Kolocouris A. Conformational energies of reference organic molecules: benchmarking of common efficient computational methods against coupled cluster theory. J Comput Aided Mol Des 2023; 37:607-656. [PMID: 37597063 PMCID: PMC10618395 DOI: 10.1007/s10822-023-00513-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/03/2023] [Indexed: 08/21/2023]
Abstract
We selected 145 reference organic molecules that include model fragments used in computer-aided drug design. We calculated 158 conformational energies and barriers using force fields, with wide applicability in commercial and free softwares and extensive application on the calculation of conformational energies of organic molecules, e.g. the UFF and DREIDING force fields, the Allinger's force fields MM3-96, MM3-00, MM4-8, the MM2-91 clones MMX and MM+, the MMFF94 force field, MM4, ab initio Hartree-Fock (HF) theory with different basis sets, the standard density functional theory B3LYP, the second-order post-HF MP2 theory and the Domain-based Local Pair Natural Orbital Coupled Cluster DLPNO-CCSD(T) theory, with the latter used for accurate reference values. The data set of the organic molecules includes hydrocarbons, haloalkanes, conjugated compounds, and oxygen-, nitrogen-, phosphorus- and sulphur-containing compounds. We reviewed in detail the conformational aspects of these model organic molecules providing the current understanding of the steric and electronic factors that determine the stability of low energy conformers and the literature including previous experimental observations and calculated findings. While progress on the computer hardware allows the calculations of thousands of conformations for later use in drug design projects, this study is an update from previous classical studies that used, as reference values, experimental ones using a variety of methods and different environments. The lowest mean error against the DLPNO-CCSD(T) reference was calculated for MP2 (0.35 kcal mol-1), followed by B3LYP (0.69 kcal mol-1) and the HF theories (0.81-1.0 kcal mol-1). As regards the force fields, the lowest errors were observed for the Allinger's force fields MM3-00 (1.28 kcal mol-1), ΜΜ3-96 (1.40 kcal mol-1) and the Halgren's MMFF94 force field (1.30 kcal mol-1) and then for the MM2-91 clones MMX (1.77 kcal mol-1) and MM+ (2.01 kcal mol-1) and MM4 (2.05 kcal mol-1). The DREIDING (3.63 kcal mol-1) and UFF (3.77 kcal mol-1) force fields have the lowest performance. These model organic molecules we used are often present as fragments in drug-like molecules. The values calculated using DLPNO-CCSD(T) make up a valuable data set for further comparisons and for improved force field parameterization.
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Affiliation(s)
- Ioannis Stylianakis
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece
| | - Nikolaos Zervos
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece
| | - Jenn-Huei Lii
- Department of Chemistry, National Changhua University of Education, Changhua City, Taiwan
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Antonios Kolocouris
- Department of Medicinal Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis Zografou, 15771, Athens, Greece.
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771, Athens, Greece.
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2
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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: 38] [Impact Index Per Article: 9.5] [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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Grisanti L, Sapunar M, Hassanali A, Došlić N. Toward Understanding Optical Properties of Amyloids: A Reaction Path and Nonadiabatic Dynamics Study. J Am Chem Soc 2020; 142:18042-18049. [DOI: 10.1021/jacs.0c07134] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luca Grisanti
- Division of Theoretical Physics, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
- Condensed Matter and Statistical Physics, International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy
| | - Marin Sapunar
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Ali Hassanali
- Condensed Matter and Statistical Physics, International Centre for Theoretical Physics, Strada Costiera 11, Trieste 34151, Italy
| | - Nađa Došlić
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
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Soorkia S, Jouvet C, Grégoire G. UV Photoinduced Dynamics of Conformer-Resolved Aromatic Peptides. Chem Rev 2019; 120:3296-3327. [DOI: 10.1021/acs.chemrev.9b00316] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Satchin Soorkia
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
| | - Christophe Jouvet
- CNRS, Aix Marseille Université, PIIM UMR 7345, 13397, Marseille, France
| | - Gilles Grégoire
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France
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5
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Lischka H, Nachtigallová D, Aquino AJA, Szalay PG, Plasser F, Machado FBC, Barbatti M. Multireference Approaches for Excited States of Molecules. Chem Rev 2018; 118:7293-7361. [DOI: 10.1021/acs.chemrev.8b00244] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, 78371 Olomouc, Czech Republic
| | - Adélia J. A. Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Péter G. Szalay
- ELTE Eötvös Loránd University, Laboratory of Theoretical Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Felix Plasser
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
- Department of Chemistry, Loughborough University, Leicestershire LE11 3TU, United Kingdom
| | - Francisco B. C. Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil
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Ben Amor N, Hoyau S, Maynau D, Brenner V. Low-lying excited states of model proteins: Performances of the CC2 method versus multireference methods. J Chem Phys 2018; 148:184105. [DOI: 10.1063/1.5025942] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Nadia Ben Amor
- CNRS, UPS, LCPQ (Laboratoire de Chimie et Physique Quantiques), IRSAMC, 118, Rte de Narbonne, F-31062 Toulouse Cedex, France
- UPS, LCPQ (Laboratoire de Chimie et Physique Quantiques), IRSAMC, Université de Toulouse, 118, Rte de Narbonne, F-31062 Toulouse Cedex, France
| | - Sophie Hoyau
- UPS, LCPQ (Laboratoire de Chimie et Physique Quantiques), IRSAMC, Université de Toulouse, 118, Rte de Narbonne, F-31062 Toulouse Cedex, France
| | - Daniel Maynau
- CNRS, UPS, LCPQ (Laboratoire de Chimie et Physique Quantiques), IRSAMC, 118, Rte de Narbonne, F-31062 Toulouse Cedex, France
- UPS, LCPQ (Laboratoire de Chimie et Physique Quantiques), IRSAMC, Université de Toulouse, 118, Rte de Narbonne, F-31062 Toulouse Cedex, France
| | - Valérie Brenner
- Laboratoire Interactions, Dynamiques et Lasers, LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette Cedex, France
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Mališ M, Došlić N. Nonradiative Relaxation Mechanisms of UV Excited Phenylalanine Residues: A Comparative Computational Study. Molecules 2017; 22:E493. [PMID: 28335582 PMCID: PMC6155328 DOI: 10.3390/molecules22030493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 03/09/2017] [Accepted: 03/16/2017] [Indexed: 11/17/2022] Open
Abstract
The present work is directed toward understanding the mechanisms of excited state deactivation in three neutral model peptides containing the phenylalanine residue. The excited state dynamics of theγL(g+)folded form of N-acetylphenylalaninylamide (NAPA B) and its amide-N-methylated derivative (NAPMA B) is reviewed and compared to the dynamics of the monohydrated structure of NAPA (NAPAH). The goal is to unravel how the environment, and in particular solvation, impacts the photodynamics of peptides. The systems are investigated using reaction path calculations and surface hopping nonadiabatic dynamics based on the coupled cluster doubles (CC2) method and time-dependent density functional theory. The work emphasizes the role that excitation transfer from the phenylππ*to amidenπ*state plays in the deactivation of the three systems and shows how the ease of out-of-plane distortions of the amide group determines the rate of population transfer between the two electronic states. The subsequent dynamics on thenπ*state is barrierless along several pathways and leads to fast deactivation to the ground electronic state.
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Affiliation(s)
- Momir Mališ
- Ruđer Bošković Institute, HR-10000 Zagreb, Croatia.
- Ecole polytechnique fédérale de Lausanne, CH-1015 Lausanne, Switzerland.
| | - Nađa Došlić
- Ruđer Bošković Institute, HR-10000 Zagreb, Croatia.
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8
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Schwing K, Gerhards M. Investigations on isolated peptides by combined IR/UV spectroscopy in a molecular beam – structure, aggregation, solvation and molecular recognition. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1229331] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Sohn WY, Brenner V, Gloaguen E, Mons M. Local NH–π interactions involving aromatic residues of proteins: influence of backbone conformation and ππ* excitation on the π H-bond strength, as revealed from studies of isolated model peptides. Phys Chem Chem Phys 2016; 18:29969-29978. [DOI: 10.1039/c6cp04109d] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Gas phase conformer-selective IR spectroscopy combined and relevant quantum chemistry methods document the NH–π interactions in Phe residues.
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Affiliation(s)
| | | | - Eric Gloaguen
- LIDYL
- CEA
- CNRS
- Université Paris-Saclay
- 91191 Gif-sur-Yvette
| | - Michel Mons
- LIDYL
- CEA
- CNRS
- Université Paris-Saclay
- 91191 Gif-sur-Yvette
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10
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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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11
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Kovač B, Ljubić I, Kivimäki A, Coreno M, Novak I. The study of the electronic structure of some N-heterocyclic carbenes (NHCs) by variable energy photoelectron spectroscopy. Phys Chem Chem Phys 2015; 17:10656-67. [DOI: 10.1039/c5cp00482a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
UV and X-ray photoelectron spectra of three N-heterocyclic carbenes under synchrotron radiation reveal details of their electronic structure and are used as a benchmark to test computational methods for treating core ionizations in systems with unusual electronic structures.
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Affiliation(s)
| | - Ivan Ljubić
- Ruđer Bošković Institute
- HR-10000 Zagreb
- Croatia
| | | | | | - Igor Novak
- Charles Sturt University
- Orange NSW 2800
- Australia
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12
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Mališ M, Loquais Y, Gloaguen E, Jouvet C, Brenner V, Mons M, Ljubić I, Došlić N. Non-radiative relaxation of UV photoexcited phenylalanine residues: probing the role of conical intersections by chemical substitution. Phys Chem Chem Phys 2014; 16:2285-8. [DOI: 10.1039/c3cp53953a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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13
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Mališ M, Loquais Y, Gloaguen E, Biswal HS, Piuzzi F, Tardivel B, Brenner V, Broquier M, Jouvet C, Mons M, Došlić N, Ljubić I. Unraveling the Mechanisms of Nonradiative Deactivation in Model Peptides Following Photoexcitation of a Phenylalanine Residue. J Am Chem Soc 2012; 134:20340-51. [DOI: 10.1021/ja3054942] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Momir Mališ
- Division
of Physical Chemistry, Ruđer Bošković Institute, Bijenička
cesta 54, HR-10002 Zagreb, Croatia
| | - Yohan Loquais
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Eric Gloaguen
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Himansu S. Biswal
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - François Piuzzi
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Benjamin Tardivel
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Valérie Brenner
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Michel Broquier
- Université Paris-Sud 11, CLUPS / CNRS, LUMAT FR 2764, Bât
106, Orsay, F-91405, France
- CNRS, Université Paris-Sud 11, ISMO, UMR 8624, Bât 210, Orsay,
F-91405, France
| | - Christophe Jouvet
- Université Paris-Sud 11, CLUPS / CNRS, LUMAT FR 2764, Bât
106, Orsay, F-91405, France
- CNRS, Université Paris-Sud 11, ISMO, UMR 8624, Bât 210, Orsay,
F-91405, France
| | - Michel Mons
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Nađa Došlić
- Division
of Physical Chemistry, Ruđer Bošković Institute, Bijenička
cesta 54, HR-10002 Zagreb, Croatia
| | - Ivan Ljubić
- Division
of Physical Chemistry, Ruđer Bošković Institute, Bijenička
cesta 54, HR-10002 Zagreb, Croatia
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Ljubić I, Sabljić A. CASSCF/CASPT2 and TD-DFT Study of Valence and Rydberg Electronic Transitions in Fluorene, Carbazole, Dibenzofuran, and Dibenzothiophene. J Phys Chem A 2011; 115:4840-50. [DOI: 10.1021/jp201618a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ivan Ljubić
- Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, P.O. Box 180, HR-10002, Zagreb, Republic of Croatia
| | - Aleksandar Sabljić
- Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, P.O. Box 180, HR-10002, Zagreb, Republic of Croatia
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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
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Revilla-López G, Laurent AD, Perpète EA, Jacquemin D, Torras J, Assfeld X, Alemán C. Key Building Block of Photoresponsive Biomimetic Systems. J Phys Chem B 2011; 115:1232-42. [DOI: 10.1021/jp108341a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Guillem Revilla-López
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal 647, 08028 Barcelona, Spain
| | - Adele D. Laurent
- Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France
| | - Eric A. Perpète
- Unité de Chimie Physique Théorique et Structurale (2742), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Denis Jacquemin
- Unité de Chimie Physique Théorique et Structurale (2742), Facultés Universitaires Notre-Dame de la Paix, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Juan Torras
- Departament d’Enginyeria Química, EUETII, Universitat Politècnica de Catalunya, Pça Rei 15, Igualada 08700, Spain
| | - Xavier Assfeld
- Chimie et Biochimie Théoriques, UMR CNRS UHP 7565, Institut Jean Barriol FR CNRS 2843, Faculté des Sciences et Techniques BP 70239, Nancy-Université, 54506 Vandoeuvre-lès-Nancy, France
| | - Carlos Alemán
- Departament d’Enginyeria Química, E. T. S. d’Enginyeria Industrial de Barcelona, Universitat Politècnica de Catalunya, Avda. Diagonal 647, 08028 Barcelona, Spain
- Center for Research in Nano-Engineering, Universitat Politècnica de Catalunya, Campus Sud, Edifici C’, C/Pasqual i Vila s/n, Barcelona E-08028, Spain
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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: 562] [Impact Index Per Article: 40.1] [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
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18
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Toroz D, van Mourik T. Structure of the gas-phase glycine tripeptide. Phys Chem Chem Phys 2010; 12:3463-73. [DOI: 10.1039/b921897a] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Šarić A, Hrenar T, Mališ M, Došlić N. Quantum mechanical study of secondary structure formation in protected dipeptides. Phys Chem Chem Phys 2010; 12:4678-85. [DOI: 10.1039/b923041f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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20
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Photophysics of the Trp-Gly dipeptide: Role of electron and proton transfer processes for efficient excited-state deactivation. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.09.087] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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