1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Osella S, Paloncýová M, Sahi M, Knippenberg S. Influence of Membrane Phase on the Optical Properties of DPH. Molecules 2020; 25:E4264. [PMID: 32957614 PMCID: PMC7570797 DOI: 10.3390/molecules25184264] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/05/2020] [Accepted: 09/14/2020] [Indexed: 11/24/2022] Open
Abstract
The fluorescent molecule diphenylhexatriene (DPH) has been often used in combination with fluorescence anisotropy measurements, yet little is known regarding the non-linear optical properties. In the current work, we focus on them and extend the application to fluorescence, while paying attention to the conformational versatility of DPH when it is embedded in different membrane phases. Extensive hybrid quantum mechanics/molecular mechanics calculations were performed to investigate the influence of the phase- and temperature-dependent lipid environment on the probe. Already, the transition dipole moments and one-photon absorption spectra obtained in the liquid ordered mixture of sphingomyelin (SM)-cholesterol (Chol) (2:1) differ largely from the ones calculated in the liquid disordered DOPC and solid gel DPPC membranes. Throughout the work, the molecular conformation in SM:Chol is found to differ from the other environments. The two-photon absorption spectra and the ones obtained by hyper-Rayleigh scattering depend strongly on the environment. Finally, a stringent comparison of the fluorescence anisotropy decay and the fluorescence lifetime confirm the use of DPH to gain information upon the surrounding lipids and lipid phases. DPH might thus open the possibility to detect and analyze different biological environments based on its absorption and emission properties.
Collapse
Affiliation(s)
- Silvio Osella
- Chemical and Biological Systems Simulation Lab, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Markéta Paloncýová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic;
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden;
| | - Maryam Sahi
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden;
| | - Stefan Knippenberg
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic;
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden;
- Theory Lab, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
| |
Collapse
|
3
|
Ortiz JV. Dyson-orbital concepts for description of electrons in molecules. J Chem Phys 2020; 153:070902. [DOI: 10.1063/5.0016472] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- J. V. Ortiz
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, USA
| |
Collapse
|
4
|
Trofimov AB, Holland DMP, Powis I, Menzies RC, Potts AW, Karlsson L, Gromov EV, Badsyuk IL, Schirmer J. Ionization of pyridine: Interplay of orbital relaxation and electron correlation. J Chem Phys 2017; 146:244307. [DOI: 10.1063/1.4986405] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- A. B. Trofimov
- Laboratory of Quantum Chemistry, Irkutsk State University, Karl Marx St. 1, 664003 Irkutsk, Russia
- Favorsky’s Institute of Chemistry, SB RAS, Favorsky St. 1, 664033 Irkutsk, Russia
| | - D. M. P. Holland
- Daresbury Laboratory, Daresbury, Warrington, Cheshire WA4 4AD, United Kingdom
| | - I. Powis
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - R. C. Menzies
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, United Kingdom
| | - A. W. Potts
- Department of Physics, King’s College, Strand, London WC2R 2LS, United Kingdom
| | - L. Karlsson
- Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - E. V. Gromov
- Max Planck Institute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
| | - I. L. Badsyuk
- Favorsky’s Institute of Chemistry, SB RAS, Favorsky St. 1, 664033 Irkutsk, Russia
| | - J. Schirmer
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 229, 69120 Heidelberg, Germany
| |
Collapse
|
5
|
Morini F, Watanabe N, Kojima M, Deleuze MS, Takahashi M. Influence of molecular vibrations on the valence electron momentum distributions of adamantane. J Chem Phys 2017. [DOI: 10.1063/1.4977060] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Filippo Morini
- Center of Molecular and Materials Modelling, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
| | - Noboru Watanabe
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Masataka Kojima
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Michael Simon Deleuze
- Center of Molecular and Materials Modelling, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
| | - Masahiko Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| |
Collapse
|
6
|
Teunissen JL, De Proft F, De Vleeschouwer F. Tuning the HOMO-LUMO Energy Gap of Small Diamondoids Using Inverse Molecular Design. J Chem Theory Comput 2017; 13:1351-1365. [PMID: 28218844 DOI: 10.1021/acs.jctc.6b01074] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Functionalized diamondoids show great potential as building blocks for various new optoelectronic applications. However, until now, only simple mono and double substitutions were investigated. In this work, we considered up to 10 and 6 sites for functionalization of the two smallest diamondoids, adamantane and diamantane, respectively, in search for diamondoid derivatives with a minimal and maximal HOMO-LUMO energy gap. To this end, the energy gap was optimized systematically using an inverse molecular design methodology based on the best-first search algorithm combined with a Monte Carlo component to escape local optima. Adamantane derivatives were found with HOMO-LUMO gaps ranging from 2.42 to 10.63 eV, with 9.45 eV being the energy gap of pure adamantane. For diamantane, similar values were obtained. The structures with the lowest HOMO-LUMO gaps showed apparent push-pull character. The push character is mainly formed by sulfur or nitrogen dopants and thiol groups, whereas the pull character is predominantly determined by the presence of electron-withdrawing nitro or carbonyl groups assisted by amino and hydroxyl groups via the formation of intramolecular hydrogen bonds. In contrast, maximal HOMO-LUMO gaps were obtained by introducing numerous electronegative groups.
Collapse
Affiliation(s)
- Jos L Teunissen
- Research Group of General Chemistry, Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Brussels, Belgium
| | - Frank De Proft
- Research Group of General Chemistry, Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Brussels, Belgium
| | - Freija De Vleeschouwer
- Research Group of General Chemistry, Vrije Universiteit Brussel (VUB) , Pleinlaan 2, 1050 Brussels, Belgium
| |
Collapse
|
7
|
Tang Y, Shan X, Niu S, Liu Z, Wang E, Watanabe N, Yamazaki M, Takahashi M, Chen X. Electron Momentum Spectroscopy Investigation of Molecular Conformations of Ethanol Considering Vibrational Effects. J Phys Chem A 2017; 121:277-287. [PMID: 27998060 DOI: 10.1021/acs.jpca.6b10009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interpretation of experimental electron momentum distributions (EMDs) of ethanol, one of the simplest molecules having conformers, has confused researchers for years. High-level calculations of Dyson orbital EMDs by thermally averaging the gauche and trans conformers as well as molecular dynamical simulations failed to quantitatively reproduce the experiments for some of the outer valence orbitals. In this work, the valence shell electron binding energy spectrum and EMDs of ethanol are revisited by the high-sensitivity electron momentum spectrometer employing symmetric noncoplanar geometry at an incident energy of 1200 eV plus binding energy, together with a detailed analysis of the influence of vibrational motions on the EMDs for the two conformers employing a harmonic analytical quantum mechanical (HAQM) approach by taking into account all of the vibrational modes. The significant discrepancies between theories and experiments in previous works have now been interpreted quantitatively, indicating that the vibrational effect plays a significant role in reproducing the experimental results, not only through the low-frequency OH and CH3 torsion modes but also through other high-frequency ones. Rational explanation of experimental momentum profiles provides solid evidence that the trans conformer is slightly more stable than the gauche conformer, in accordance with thermodynamic predictions and other experiments. The case of ethanol demonstrates the significance of considering vibrational effects when performing a conformational study on flexible molecules using electron momentum spectroscopy.
Collapse
Affiliation(s)
- Yaguo Tang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Xu Shan
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Shanshan Niu
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Zhaohui Liu
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Enliang Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China , Hefei, Anhui 230026, China
| | - Noboru Watanabe
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University , Sendai 980-8577, Japan
| | - Masakazu Yamazaki
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University , Sendai 980-8577, Japan
| | - Masahiko Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University , Sendai 980-8577, Japan
| | - Xiangjun Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China , Hefei, Anhui 230026, China
| |
Collapse
|
8
|
Morini F, Watanabe N, Kojima M, Deleuze MS, Takahashi M. Electron momentum spectroscopy of dimethyl ether taking account of nuclear dynamics in the electronic ground state. J Chem Phys 2015; 143:134309. [PMID: 26450316 DOI: 10.1063/1.4931918] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The influence of nuclear dynamics in the electronic ground state on the (e,2e) momentum profiles of dimethyl ether has been analyzed using the harmonic analytical quantum mechanical and Born-Oppenheimer molecular dynamics approaches. In spite of fundamental methodological differences, results obtained with both approaches consistently demonstrate that molecular vibrations in the electronic ground state have a most appreciable influence on the momentum profiles associated to the 2b1, 6a1, 4b2, and 1a2 orbitals. Taking this influence into account considerably improves the agreement between theoretical and newly obtained experimental momentum profiles, with improved statistical accuracy. Both approaches point out in particular the most appreciable role which is played by a few specific molecular vibrations of A1, B1, and B2 symmetries, which correspond to C-H stretching and H-C-H bending modes. In line with the Herzberg-Teller principle, the influence of these molecular vibrations on the computed momentum profiles can be unraveled from considerations on the symmetry characteristics of orbitals and their energy spacing.
Collapse
Affiliation(s)
- Filippo Morini
- Center of Molecular and Materials Modelling, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
| | - Noboru Watanabe
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Masataka Kojima
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Michael Simon Deleuze
- Center of Molecular and Materials Modelling, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
| | - Masahiko Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| |
Collapse
|
9
|
Morini F, Deleuze MS, Watanabe N, Takahashi M. Theoretical study of molecular vibrations in electron momentum spectroscopy experiments on furan: an analytical versus a molecular dynamical approach. J Chem Phys 2015; 142:094308. [PMID: 25747082 DOI: 10.1063/1.4913642] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The influence of thermally induced nuclear dynamics (molecular vibrations) in the initial electronic ground state on the valence orbital momentum profiles of furan has been theoretically investigated using two different approaches. The first of these approaches employs the principles of Born-Oppenheimer molecular dynamics, whereas the so-called harmonic analytical quantum mechanical approach resorts to an analytical decomposition of contributions arising from quantized harmonic vibrational eigenstates. In spite of their intrinsic differences, the two approaches enable consistent insights into the electron momentum distributions inferred from new measurements employing electron momentum spectroscopy and an electron impact energy of 1.2 keV. Both approaches point out in particular an appreciable influence of a few specific molecular vibrations of A1 symmetry on the 9a1 momentum profile, which can be unravelled from considerations on the symmetry characteristics of orbitals and their energy spacing.
Collapse
Affiliation(s)
- Filippo Morini
- Center of Molecular and Materials Modelling, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
| | - Michael S Deleuze
- Center of Molecular and Materials Modelling, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
| | - Noboru Watanabe
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| | - Masahiko Takahashi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai 980-8577, Japan
| |
Collapse
|
10
|
Yang J, Shan X, Zhang Z, Tang Y, Zhao M, Chen X. Ring-puckering effects on electron momentum distributions of valence orbitals of oxetane. J Phys Chem A 2014; 118:11780-6. [PMID: 25423196 DOI: 10.1021/jp509526a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The binding energy spectra and electron momentum distributions for the outer-valence molecular orbitals of oxetane have been measured utilizing (e, 2e) electron momentum spectrometer with non-coplanar asymmetric geometry at the impact energy of 2500 eV. The experimental momentum distributions were compared with the density functional theory calculations employing B3LYP hybrid functional with aug-cc-pVTZ basis set. It was found that the calculation at planar geometry (C2v) completely fails to interpret the large "turn-up" at low momentum region in electron momentum distribution of the highest occupied molecular orbital (HOMO) 3b1, while the calculations considering the thermal abundances of planar (C2v) and bent (Cs) conformers or the thermally populated vibrational states of ring-puckering motion have significantly improved the agreement. The results indicate that the ring-puckering motion of oxetane has a strong effect on the electron density distribution of HOMO.
Collapse
Affiliation(s)
- Jing Yang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Modern Physics, University of Science and Technology of China , 96 Jinzhai Road, Hefei, Anhui 230026, China
| | | | | | | | | | | |
Collapse
|
11
|
Wang EL, Shi YF, Shan X, Yang HJ, Zhang W, Chen XJ. Electron Momentum Spectroscopy of Valence Orbitals of n-Propyl Iodide: Spin-Orbit Coupling Effect and Intramolecular Orbital Interaction. CHINESE J CHEM PHYS 2014. [DOI: 10.1063/1674-0068/27/05/503-511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
|
12
|
Shojaei SHR, Vandenbussche J, Deleuze MS, Bultinck P. Electron momentum spectroscopy of 1-butene: a theoretical analysis using molecular dynamics and molecular quantum similarity. J Phys Chem A 2013; 117:8388-98. [PMID: 23902590 DOI: 10.1021/jp405122p] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The results of experimental studies of the valence electronic structure of 1-butene by means of electron momentum spectroscopy (EMS) have been reinterpreted on the basis of molecular dynamical simulations in conjunction with the classical MM3 force field. The computed atomic trajectories demonstrate the importance of thermally induced nuclear dynamics in the electronic neutral ground state, in the form of significant deviations from stationary points on the potential energy surface and considerable variations of the C-C-C-C dihedral angle. These motions are found to have a considerable influence on the computed spectral bands and outer-valence electron momentum distributions. Euclidean distances between spherically averaged electron momentum densities confirm that thermally induced nuclear motions need to be fully taken into account for a consistent interpretation of the results of EMS experiments on conformationally flexible molecules.
Collapse
Affiliation(s)
- S H Reza Shojaei
- Research Group of Theoretical Chemistry and Molecular Modelling, Hasselt University, Agoralaan, Gebouw D, B-3590 Diepenbeek, Belgium
| | | | | | | |
Collapse
|
13
|
Shojaei SHR, Morini F, Deleuze MS. Photoelectron and electron momentum spectroscopy of tetrahydrofuran from a molecular dynamical perspective. J Phys Chem A 2013; 117:1918-29. [PMID: 23387306 DOI: 10.1021/jp310722a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The results of experimental studies of the valence electronic structure of tetrahydrofuran employing He I photoelectron spectroscopy as well as Electron Momentum Spectroscopy (EMS) have been reinterpreted on the basis of Molecular Dynamical simulations employing the classical MM3 force field and large-scale quantum mechanical simulations employing Born-Oppenheimer Molecular Dynamics in conjunction with the dispersion corrected ωB97XD exchange-correlation functional. Analysis of the produced atomic trajectories demonstrates the importance of thermal deviations from the lowest energy path for pseudorotation, in the form of considerable variations of the ring-puckering amplitude. These deviations are found to have a significant influence on several outer-valence electron momentum distributions, as well as on the He I photoelectron spectrum.
Collapse
Affiliation(s)
- S H Reza Shojaei
- Research Group of Theoretical Chemistry and Molecular Modelling, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
| | | | | |
Collapse
|
14
|
Potts A, Holland D, Powis I, Karlsson L, Trofimov A, Bodzuk I. A study of the valence shell electronic structure and photoionisation dynamics of meta-dichlorobenzene and meta-bromochlorobenzene. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2012.12.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
15
|
A study of the valence shell electronic structure and photoionisation dynamics of para-dichlorobenzene and para-bromochlorobenzene. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2012.09.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
16
|
Wang C, Chen Z, Wu W, Mo Y. How the Generalized Anomeric Effect Influences the Conformational Preference. Chemistry 2012; 19:1436-44. [DOI: 10.1002/chem.201203429] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Indexed: 11/12/2022]
|
17
|
Huang C, Shan X, Zhang Z, Wang E, Li Z, Chen X. High-resolution electron momentum spectroscopy of valence satellites of carbon disulfide. J Chem Phys 2010; 133:124303. [DOI: 10.1063/1.3481778] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
|
18
|
Morini F, Hajgató B, Deleuze MS. Electron Momentum Spectroscopy of Norbornadiene at the Benchmark ADC(3) Level. J Phys Chem A 2010; 114:9374-87. [DOI: 10.1021/jp105551j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Filippo Morini
- Research Group of Theoretical Chemistry and Molecular Modelling, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
| | - Balázs Hajgató
- Research Group of Theoretical Chemistry and Molecular Modelling, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
| | - Michael S. Deleuze
- Research Group of Theoretical Chemistry and Molecular Modelling, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium
| |
Collapse
|
19
|
Morini F, Knippenberg S, Deleuze MS, Hajgató B. Quantum Chemical Study of Conformational Fingerprints in the Photoelectron Spectra and (e, 2e) Electron Momentum Distributions of n-Hexane. J Phys Chem A 2010; 114:4400-17. [DOI: 10.1021/jp9116358] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- F. Morini
- Group of Theoretical Chemistry and Molecular Modelling, Department SBG, Hasselt University, Agoralaan, Gebouw D, B-3590 Diepenbeek, Belgium
| | - S. Knippenberg
- Group of Theoretical Chemistry and Molecular Modelling, Department SBG, Hasselt University, Agoralaan, Gebouw D, B-3590 Diepenbeek, Belgium
| | - M. S. Deleuze
- Group of Theoretical Chemistry and Molecular Modelling, Department SBG, Hasselt University, Agoralaan, Gebouw D, B-3590 Diepenbeek, Belgium
| | - B. Hajgató
- Group of Theoretical Chemistry and Molecular Modelling, Department SBG, Hasselt University, Agoralaan, Gebouw D, B-3590 Diepenbeek, Belgium
| |
Collapse
|
20
|
Chein RJ, Corey EJ. Strong Conformational Preferences of Heteroaromatic Ethers and Electron Pair Repulsion. Org Lett 2010; 12:132-5. [DOI: 10.1021/ol9025364] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rong-Jie Chein
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, and Institute of Chemistry, Academia Sinica, 115 Nankang, Taipei, Taiwan
| | - E. J. Corey
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, and Institute of Chemistry, Academia Sinica, 115 Nankang, Taipei, Taiwan
| |
Collapse
|
21
|
Kunitski M, Knippenberg S, Gelin M, Riehn C, Dreuw A, Brutschy B. Ring-puckering motion in cyclopentene studied by time-resolved rotational coherence spectroscopy and ab initio calculations. Phys Chem Chem Phys 2010; 12:8190-200. [DOI: 10.1039/b925388b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
22
|
Computational studies of the role of glycopyranosyl oxacarbenium ions in glycobiology and glycochemistry. Adv Carbohydr Chem Biochem 2009; 62:83-159. [PMID: 19501705 DOI: 10.1016/s0065-2318(09)00004-3] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
23
|
Hajgató B, Deleuze MS, Morini F. Probing Nuclear Dynamics in Momentum Space: A New Interpretation of (e, 2e) Electron Impact Ionization Experiments on Ethanol. J Phys Chem A 2009; 113:7138-54. [DOI: 10.1021/jp9027029] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Balázs Hajgató
- Research Group of Theoretical Chemistry, Department SBG, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium, and Eenheid Algemene Chemie, Vrije Universiteit Brussel, Faculteit Wetenschappen, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Michael S. Deleuze
- Research Group of Theoretical Chemistry, Department SBG, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium, and Eenheid Algemene Chemie, Vrije Universiteit Brussel, Faculteit Wetenschappen, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Filippo Morini
- Research Group of Theoretical Chemistry, Department SBG, Hasselt University, Agoralaan Gebouw D, B-3590 Diepenbeek, Belgium, and Eenheid Algemene Chemie, Vrije Universiteit Brussel, Faculteit Wetenschappen, Pleinlaan 2, B-1050 Brussels, Belgium
| |
Collapse
|
24
|
Ning CG, Huang YR, Zhang SF, Deng JK, Liu K, Luo ZH, Wang F. Experimental and Theoretical Electron Momentum Spectroscopic Study of the Valence Electronic Structure of Tetrahydrofuran under Pseudorotation. J Phys Chem A 2008; 112:11078-87. [DOI: 10.1021/jp8038658] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- C. G. Ning
- Department of Physics and Key Laboratory of Atomic and Molecular NanoSciences of MOE, Tsinghua University, Beijing 100084, People’s Republic of China, and Centre for Molecular Simulation, Swinburne University of Technology, P.O. Box 218, Hawthorn, Melbourne, Victoria 3122, Australia
| | - Y. R. Huang
- Department of Physics and Key Laboratory of Atomic and Molecular NanoSciences of MOE, Tsinghua University, Beijing 100084, People’s Republic of China, and Centre for Molecular Simulation, Swinburne University of Technology, P.O. Box 218, Hawthorn, Melbourne, Victoria 3122, Australia
| | - S. F. Zhang
- Department of Physics and Key Laboratory of Atomic and Molecular NanoSciences of MOE, Tsinghua University, Beijing 100084, People’s Republic of China, and Centre for Molecular Simulation, Swinburne University of Technology, P.O. Box 218, Hawthorn, Melbourne, Victoria 3122, Australia
| | - J. K. Deng
- Department of Physics and Key Laboratory of Atomic and Molecular NanoSciences of MOE, Tsinghua University, Beijing 100084, People’s Republic of China, and Centre for Molecular Simulation, Swinburne University of Technology, P.O. Box 218, Hawthorn, Melbourne, Victoria 3122, Australia
| | - K. Liu
- Department of Physics and Key Laboratory of Atomic and Molecular NanoSciences of MOE, Tsinghua University, Beijing 100084, People’s Republic of China, and Centre for Molecular Simulation, Swinburne University of Technology, P.O. Box 218, Hawthorn, Melbourne, Victoria 3122, Australia
| | - Z. H. Luo
- Department of Physics and Key Laboratory of Atomic and Molecular NanoSciences of MOE, Tsinghua University, Beijing 100084, People’s Republic of China, and Centre for Molecular Simulation, Swinburne University of Technology, P.O. Box 218, Hawthorn, Melbourne, Victoria 3122, Australia
| | - F. Wang
- Department of Physics and Key Laboratory of Atomic and Molecular NanoSciences of MOE, Tsinghua University, Beijing 100084, People’s Republic of China, and Centre for Molecular Simulation, Swinburne University of Technology, P.O. Box 218, Hawthorn, Melbourne, Victoria 3122, Australia
| |
Collapse
|
25
|
Morini F, Hajgató B, Deleuze MS, Ning CG, Deng JK. Benchmark Dyson Orbital Study of the Ionization Spectrum and Electron Momentum Distributions of Ethanol in Conformational Equilibrium. J Phys Chem A 2008; 112:9083-96. [DOI: 10.1021/jp804284p] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
|
26
|
Huang YR, Hajgató B, Ning CG, Zhang SF, Liu K, Luo ZH, Deng JK, Deleuze MS. Study of the Valence Wave Function of Thiophene with High Resolution Electron Momentum Spectroscopy and Advanced Dyson Orbital Theories. J Phys Chem A 2008; 112:2339-54. [DOI: 10.1021/jp710845n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Y. R. Huang
- Department of Physics and Key Laboratory of Atomic and Molecular NanoSciences of MOE, Tsinghua University, Beijing 100084, P. R. China, and Research Group of Theoretical Chemistry, Department SBG, Hasselt University, Agoralaan, Gebouw D, B-3590 Diepenbeek, Belgium
| | - B. Hajgató
- Department of Physics and Key Laboratory of Atomic and Molecular NanoSciences of MOE, Tsinghua University, Beijing 100084, P. R. China, and Research Group of Theoretical Chemistry, Department SBG, Hasselt University, Agoralaan, Gebouw D, B-3590 Diepenbeek, Belgium
| | - C. G. Ning
- Department of Physics and Key Laboratory of Atomic and Molecular NanoSciences of MOE, Tsinghua University, Beijing 100084, P. R. China, and Research Group of Theoretical Chemistry, Department SBG, Hasselt University, Agoralaan, Gebouw D, B-3590 Diepenbeek, Belgium
| | - S. F. Zhang
- Department of Physics and Key Laboratory of Atomic and Molecular NanoSciences of MOE, Tsinghua University, Beijing 100084, P. R. China, and Research Group of Theoretical Chemistry, Department SBG, Hasselt University, Agoralaan, Gebouw D, B-3590 Diepenbeek, Belgium
| | - K. Liu
- Department of Physics and Key Laboratory of Atomic and Molecular NanoSciences of MOE, Tsinghua University, Beijing 100084, P. R. China, and Research Group of Theoretical Chemistry, Department SBG, Hasselt University, Agoralaan, Gebouw D, B-3590 Diepenbeek, Belgium
| | - Z. H. Luo
- Department of Physics and Key Laboratory of Atomic and Molecular NanoSciences of MOE, Tsinghua University, Beijing 100084, P. R. China, and Research Group of Theoretical Chemistry, Department SBG, Hasselt University, Agoralaan, Gebouw D, B-3590 Diepenbeek, Belgium
| | - J. K. Deng
- Department of Physics and Key Laboratory of Atomic and Molecular NanoSciences of MOE, Tsinghua University, Beijing 100084, P. R. China, and Research Group of Theoretical Chemistry, Department SBG, Hasselt University, Agoralaan, Gebouw D, B-3590 Diepenbeek, Belgium
| | - M. S. Deleuze
- Department of Physics and Key Laboratory of Atomic and Molecular NanoSciences of MOE, Tsinghua University, Beijing 100084, P. R. China, and Research Group of Theoretical Chemistry, Department SBG, Hasselt University, Agoralaan, Gebouw D, B-3590 Diepenbeek, Belgium
| |
Collapse
|
27
|
Huang YR, Ning CG, Deng JK, Deleuze MS. Study of the photoelectron and electron momentum spectra of cyclopentene using benchmark Dyson orbital theories. Phys Chem Chem Phys 2008; 10:2374-89. [DOI: 10.1039/b718588j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
28
|
Ning C, Hajgató B, Huang Y, Zhang S, Liu K, Luo Z, Knippenberg S, Deng J, Deleuze M. High resolution electron momentum spectroscopy of the valence orbitals of water. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2007.09.030] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
29
|
Knippenberg S, Huang YR, Hajgató B, François JP, Deng JK, Deleuze MS. Probing molecular conformations in momentum space: The case of n-pentane. J Chem Phys 2007; 127:174306. [DOI: 10.1063/1.2772848] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
|
30
|
Knippenberg S, Hajgató B, François JP, Deleuze MS. Theoretical Study of the Fragmentation Pathways of Norbornane in Its Doubly Ionized Ground State. J Phys Chem A 2007; 111:10834-48. [DOI: 10.1021/jp074207r] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Stefan Knippenberg
- Theoretical Chemistry, Department SBG, Hasselt University, Agoralaan, Gebouw D, B-3590 Diepenbeek, Belgium
| | - Balázs Hajgató
- Theoretical Chemistry, Department SBG, Hasselt University, Agoralaan, Gebouw D, B-3590 Diepenbeek, Belgium
| | - Jean-Pierre François
- Theoretical Chemistry, Department SBG, Hasselt University, Agoralaan, Gebouw D, B-3590 Diepenbeek, Belgium
| | - Michael S. Deleuze
- Theoretical Chemistry, Department SBG, Hasselt University, Agoralaan, Gebouw D, B-3590 Diepenbeek, Belgium
| |
Collapse
|