1
|
Ariai J, Gellrich U. The entropic penalty for associative reactions and their physical treatment during routine computations. Phys Chem Chem Phys 2023; 25:14005-14015. [PMID: 37161492 DOI: 10.1039/d3cp00970j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A systematic study of the entropic penalty for associative reactions is presented. It is shown that computed solution-phase Gibbs free energies typically overestimate entropic contributions. This entropic penalty for associative reactions in solution, i.e., if the number of particles decreases along the reaction coordinate (sum of stoichiometric numbers ), originates from the insufficient treatment of entropic effects by implicit solvent models. We propose an additive correction scheme to Gibbs free energies that is suitable for routine applications by non-expert users. This correction is based on Garza's formalism for the solution-phase entropy [A. J. Garza, J. Chem. Theory Comput., 2019, 15, 3204.] that is physically sound and embedded into an efficient black-box type algorithm. To critically evaluate the entropic penalty and its proposed treatment, we compiled an experimental benchmark set of 31 ΔrG and 22 in 15 different solvents. Using a representative best-practice computational protocol (at wave function theory (WFT) based DLPNO-CCSD(T) and density functional theory (DFT) based revDSD-PBEP86-D4 level with an implicit solvent model), we determined a sizeable entropic penalty ranging from 2-11 kcal mol-1. Using the correction scheme presented herein, the entropic penalty is corrected to the chemical accuracy of ≤1 kcal mol-1 (WFT and DFT). The same applies to at the WFT level. Barriers at the DFT level are overestimated by 2 kcal mol-1 (classic) and underestimated by 2 kcal mol-1 (corrected). This effect is attributed to the finding that barriers computed at the DFT level are systematically 2-3 kcal mol-1 lower than barriers obtained with WFT.
Collapse
Affiliation(s)
- Jama Ariai
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.
| | - Urs Gellrich
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.
| |
Collapse
|
2
|
Bolmatenkov DN, Notfullin AA, Yagofarov MI, Nagrimanov RN, Italmasov AR, Solomonov BN. Vaporization thermodynamics of normal alkyl phenones. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2022.121000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
3
|
Santra G, Martin JM. Performance of Localized-Orbital Coupled-Cluster Approaches for the Conformational Energies of Longer n-Alkane Chains. J Phys Chem A 2022; 126:9375-9391. [PMID: 36508714 PMCID: PMC9791657 DOI: 10.1021/acs.jpca.2c06407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report an update and enhancement of the ACONFL (conformer energies of large alkanes [J. Phys. Chem. A2022,126, 3521-3535]) dataset. For the ACONF12 (n-dodecane) subset, we report basis set limit canonical coupled-cluster with singles, doubles, and perturbative triples [i.e., CCSD(T)] reference data obtained from the MP2-F12/cc-pV{T,Q}Z-F12 extrapolation, [CCSD(F12*)-MP2-F12]/aug-cc-pVTZ-F12, and a (T) correction from conventional CCSD(T)/aug-cc-pV{D,T}Z calculations. Then, we explored the performance of a variety of single and composite localized-orbital CCSD(T) approximations, ultimately finding an affordable localized natural orbital CCSD(T) [LNO-CCSD(T)]-based post-MP2 correction that agrees to 0.006 kcal/mol mean absolute deviation with the revised canonical reference data. In tandem with canonical MP2-F12 complete basis set extrapolation, this was then used to re-evaluate the ACONF16 and ACONF20 subsets for n-hexadecane and n-icosane, respectively. Combining those with the revised canonical reference data for the dodecane conformers (i.e., ACONF12 subset), a revised ACONFL set was obtained. It was then used to assess the performance of different localized-orbital coupled-cluster approaches, such as pair natural orbital localized CCSD(T) [PNO-LCCSD(T)] as implemented in MOLPRO, DLPNO-CCSD(T0) and DLPNO-CCSD(T1) as implemented in ORCA, and LNO-CCSD(T) as implemented in MRCC, at their respective "Normal", "Tight", "vTight", and "vvTight" accuracy settings. For a given accuracy threshold and basis set, DLPNO-CCSD(T1) and DLPNO-CCSD(T0) perform comparably. With "VeryTightPNO" cutoffs, explicitly correlated DLPNO-CCSD(T1)-F12/VDZ-F12 is the best pick among all the DLPNO-based methods tested. To isolate basis set incompleteness from localized-orbital-related truncation errors (domain, LNOs), we have also compared the localized coupled-cluster approaches with canonical DF-CCSD(T)/aug-cc-pVTZ for the ACONF12 set. We found that gradually tightening the cutoffs improves the performance of LNO-CCSD(T), and using a composite scheme such as vTight + 0.50[vTight - Tight] improves things further. For DLPNO-CCSD(T1), "TightPNO" and "VeryTightPNO" offer a statistically similar accuracy, which gets slightly better when TCutPNO is extrapolated to the complete PNO space limit. Similar to Brauer et al.'s [Phys. Chem. Chem. Phys.2016,18 (31), 20905-20925] previous report for the S66x8 noncovalent interactions, the dispersion-corrected direct random phase approximation (dRPA)-based double hybrids perform remarkably well for the ACONFL set. While the revised reference data do not affect any conclusions on the less accurate methods, they may upend orderings for more accurate methods with error statistics on the same order as the difference between reference datasets.
Collapse
|
4
|
Ghahremanpour MM, Tirado-Rives J, Jorgensen WL. Refinement of the Optimized Potentials for Liquid Simulations Force Field for Thermodynamics and Dynamics of Liquid Alkanes. J Phys Chem B 2022; 126:5896-5907. [PMID: 35914179 PMCID: PMC9939004 DOI: 10.1021/acs.jpcb.2c03686] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Torsion and Lennard-Jones parameters of the optimized potentials for liquid simulations (OPLS) all-atom force field have been refined for describing thermodynamics and dynamics of a wide range of liquid alkanes. Monte Carlo statistical mechanics (MC) and molecular dynamics (MD) simulations were carried out. For thermodynamics properties, MC simulations with truncated electrostatic interactions performed very closely to MD simulations with a Verlet neighbor list and the particle mesh Ewald algorithm. The average errors in comparison with experimental data for computed properties were improved with the modified force field (OPLS/2020), especially for long-chain alkanes. For liquid densities, heats of vaporization, and free energies of hydration, the average errors are 0.01 g/cm3, 0.2 kcal/mol, and ca. 0.5 kcal/mol, respectively; significant gains were made for relative heats of vaporization of isomeric series. Results for self-diffusion coefficients also reproduce experimental data well for linear alkane liquids up to hexadecane. The new force field is suitable for use in improved modeling of myriad systems of importance in chemistry, biology, and materials science.
Collapse
Affiliation(s)
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - William L. Jorgensen
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| |
Collapse
|
5
|
Ehlert S, Grimme S, Hansen A. Conformational Energy Benchmark for Longer n-Alkane Chains. J Phys Chem A 2022; 126:3521-3535. [PMID: 35616628 DOI: 10.1021/acs.jpca.2c02439] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the first benchmark set focusing on the conformational energies of highly flexible, long n-alkane chains, termed ACONFL. Unbranched alkanes are ubiquitous building blocks in nature, so the goal is to be able to calculate their properties most accurately to improve the modeling of, e.g., complex (biological) systems. Very accurate DLPNO-CCSD(T1)/CBS reference values are provided, which allow for a statistical meaningful evaluation of even the best available density functional methods. The performance of established and modern (dispersion corrected) density functionals is comprehensively assessed. The recently introduced r2SCAN-V functional shows excellent performance, similar to efficient composite DFT methods like B97-3c and r2SCAN-3c, which provide an even better cost-accuracy ratio, while almost reaching the accuracy of much more computationally demanding hybrid or double hybrid functionals with large QZ AO basis sets. In addition, we investigated the performance of common wave function methods, where MP2/CBS surprisingly performs worse compared to the simple D4 dispersion corrected Hartree-Fock. Furthermore, we investigate the performance of several semiempirical and force field methods, which are commonly used for the generation of conformational ensembles in multilevel workflows or in large scale molecular dynamics studies. Outstanding performance is obtained by the recently introduced general force field, GFN-FF, while other commonly applied methods like the universal force field yield large errors. We recommend the ACONFL as a helpful benchmark set for parametrization of new semiempirical or force field methods and machine learning potentials as well as a meaningful validation set for newly developed DFT or dispersion methods.
Collapse
Affiliation(s)
- Sebastian Ehlert
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
| |
Collapse
|
6
|
Zheng P, Yang W, Wu W, Isayev O, Dral PO. Toward Chemical Accuracy in Predicting Enthalpies of Formation with General-Purpose Data-Driven Methods. J Phys Chem Lett 2022; 13:3479-3491. [PMID: 35416675 DOI: 10.1021/acs.jpclett.2c00734] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Enthalpies of formation and reaction are important thermodynamic properties that have a crucial impact on the outcome of chemical transformations. Here we implement the calculation of enthalpies of formation with a general-purpose ANI-1ccx neural network atomistic potential. We demonstrate on a wide range of benchmark sets that both ANI-1ccx and our other general-purpose data-driven method AIQM1 approach the coveted chemical accuracy of 1 kcal/mol with the speed of semiempirical quantum mechanical methods (AIQM1) or faster (ANI-1ccx). It is remarkably achieved without specifically training the machine learning parts of ANI-1ccx or AIQM1 on formation enthalpies. Importantly, we show that these data-driven methods provide statistical means for uncertainty quantification of their predictions, which we use to detect and eliminate outliers and revise reference experimental data. Uncertainty quantification may also help in the systematic improvement of such data-driven methods.
Collapse
Affiliation(s)
- Peikun Zheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Wudi Yang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Wei Wu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Olexandr Isayev
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Pavlo O Dral
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Department of Chemistry, and College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| |
Collapse
|
7
|
Basu A, Mookherjee M, McMahan E, Haberl B, Boehler R. Behavior of Long-Chain Hydrocarbons at High Pressures and Temperatures. J Phys Chem B 2022; 126:2530-2537. [PMID: 35332775 DOI: 10.1021/acs.jpcb.1c10786] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although long-chain aliphatic hydrocarbons are documented in meteorites, their origin is poorly understood. A key question is whether they are pristine or a byproduct of terrestrial alteration? To understand if these long-chain hydrocarbons are indigenous, it will be important to explore their thermodynamic and mechanical stability at conditions experienced by extraterrestrial objects during atmospheric entry and passage. Extreme pressures and temperatures experienced by meteorites are likely to alter the molecular organization of these long-chain hydrocarbons. These structural changes associated with extreme conditions are often documented via laboratory-based Raman spectroscopic measurements. So far, Raman spectroscopic measurements have investigated the effect of static compression on the aliphatic hydrocarbons. The effect of temperature on the structural changes remains poorly explored. To bridge this gap, in this study, we have explored the behavior of two aliphatic hydrocarbons at simultaneously high pressures and temperatures. We have used a resistively heated diamond anvil cell. On compression to moderate pressures, the appearance of new vibrational modes in the low-energy region confirms prior studies and is related to the bending of the linear chains. Upon heating to ∼220 °C, we note that the new low-energy mode undergoes softening. The mode softening is likely due to the combination of unbending of the alkane chain and mode anharmonicity.
Collapse
Affiliation(s)
- Abhisek Basu
- Earth Materials Laboratory, Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida 32306, United States
| | - Mainak Mookherjee
- Earth Materials Laboratory, Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida 32306, United States
| | - Ericka McMahan
- Earth Materials Laboratory, Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida 32306, United States
| | - Bianca Haberl
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Reinhard Boehler
- Neutron Scattering Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| |
Collapse
|
8
|
Espinosa-Dzib A, Vyazovkin S. Nanoconfined gelation in systems based on stearic and 12-hydroxystearic acids: A calorimetric study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
9
|
Peresypkina E, Grill K, Hiltl B, Virovets AV, Kremer W, Hilgert J, Tremel W, Scheer M. Die Dreikomponenten‐Selbstorganisation ändert ihre Richtung: Ein Sprung von einfachen Polymeren zu 3D‐Netzwerken sphärischer Wirt/Gast‐Aggregate. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Eugenia Peresypkina
- Institut für Anorganische Chemie Universität Regensburg 93040 Regensburg Deutschland
| | - Kevin Grill
- Institut für Anorganische Chemie Universität Regensburg 93040 Regensburg Deutschland
| | - Barbara Hiltl
- Institut für Anorganische Chemie Universität Regensburg 93040 Regensburg Deutschland
| | - Alexander V. Virovets
- Institut für Anorganische Chemie Universität Regensburg 93040 Regensburg Deutschland
| | - Werner Kremer
- Institut für Biophysik und Physikalische Biochemie Universität Regensburg 93040 Regensburg Deutschland
| | - Jan Hilgert
- Institut für Anorganische Chemie und Analytische Chemie Universität Mainz 55128 Mainz Deutschland
| | - Wolfgang Tremel
- Institut für Anorganische Chemie und Analytische Chemie Universität Mainz 55128 Mainz Deutschland
| | - Manfred Scheer
- Institut für Anorganische Chemie Universität Regensburg 93040 Regensburg Deutschland
| |
Collapse
|
10
|
Peresypkina E, Grill K, Hiltl B, Virovets AV, Kremer W, Hilgert J, Tremel W, Scheer M. Three-Component Self-Assembly Changes its Course: A Leap from Simple Polymers to 3D Networks of Spherical Host-Guest Assemblies. Angew Chem Int Ed Engl 2021; 60:12132-12142. [PMID: 33686782 PMCID: PMC8252601 DOI: 10.1002/anie.202103178] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Indexed: 11/20/2022]
Abstract
One‐pot self‐assembly reactions of the polyphosphorus complex [Cp*Fe(η5‐P5)] (A), a coinage metal salt AgSbF6, and flexible aliphatic dinitriles NC(CH2)xCN (x=1–10) yield 1D, 2D, and 3D coordination polymers. The seven‐membered backbone of the dinitrile was experimentally found as the borderline for the self‐assembly system furnishing products of different kinds. At x<7, various rather simple polymers are exclusively formed possessing either 0D or 1D Ag/A structural motifs connected by dinitrile spacers, while at x≥7, the self‐assembly switches to unprecedented extraordinary 3D networks of nano‐sized host–guest assemblies (SbF6)@[(A)9Ag11]11+ (x=7) or (A)@[(A)12Ag12]12+ (x=8–10) linked by dinitriles. The polycationic nodes represent the first superspheres based on A and silver and are host–guest able. All products are characterized by NMR spectroscopy, mass spectrometry, and single‐crystal X‐ray diffraction. The assemblies [(A)12Ag12]12+ were visualized by transmission electron microscopy.
Collapse
Affiliation(s)
- Eugenia Peresypkina
- Institute of Inorganic Chemistry, University of Regensburg, 93040, Regensburg, Germany
| | - Kevin Grill
- Institute of Inorganic Chemistry, University of Regensburg, 93040, Regensburg, Germany
| | - Barbara Hiltl
- Institute of Inorganic Chemistry, University of Regensburg, 93040, Regensburg, Germany
| | - Alexander V Virovets
- Institute of Inorganic Chemistry, University of Regensburg, 93040, Regensburg, Germany
| | - Werner Kremer
- Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040, Regensburg, Germany
| | - Jan Hilgert
- Institute of Inorganic Chemistry and Analytical Chemistry, University of Mainz, 55128, Mainz, Germany
| | - Wolfgang Tremel
- Institute of Inorganic Chemistry and Analytical Chemistry, University of Mainz, 55128, Mainz, Germany
| | - Manfred Scheer
- Institute of Inorganic Chemistry, University of Regensburg, 93040, Regensburg, Germany
| |
Collapse
|
11
|
Pracht P, Grimme S. Calculation of absolute molecular entropies and heat capacities made simple. Chem Sci 2021; 12:6551-6568. [PMID: 34040731 PMCID: PMC8139639 DOI: 10.1039/d1sc00621e] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/24/2021] [Indexed: 12/25/2022] Open
Abstract
We propose a fully-automated composite scheme for the accurate and numerically stable calculation of molecular entropies by efficiently combining density-functional theory (DFT), semi-empirical methods (SQM), and force-field (FF) approximations. The scheme is systematically expandable and can be integrated seamlessly with continuum-solvation models. Anharmonic effects are included through the modified rigid-rotor-harmonic-oscillator (msRRHO) approximation and the Gibbs-Shannon formula for extensive conformer ensembles (CEs), which are generated by a metadynamics search algorithm and are extrapolated to completeness. For the first time, variations of the ro-vibrational entropy over the CE are consistently accounted-for through a Boltzmann-population average. Extensive tests of the protocol with the two standard DFT approaches B97-3c and B3LYP-D3 reveal an unprecedented accuracy with mean deviations <1 cal mol-1 K-1 (about <1-2%) for the total gas phase molecular entropy of medium-sized molecules. Even for the hardship case of extremely flexible linear alkanes (C14H30-C16H34), errors are only about 3 cal mol-1 K-1. Comprehensive tests indicate a relatively strong variation of the conformational entropy on the underlying level of theory for typical drug molecules, inferring the complex potential energy surfaces as the main source of error. Furthermore, we show some application examples for the calculation of free energy differences in typical chemical reactions.
Collapse
Affiliation(s)
- Philipp Pracht
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn Beringstr. 4 53115 Bonn Germany +49-228-73-2351
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn Beringstr. 4 53115 Bonn Germany +49-228-73-2351
| |
Collapse
|
12
|
Farrell A, González-Jiménez M, Ramakrishnan G, Wynne K. Low-Frequency (Gigahertz to Terahertz) Depolarized Raman Scattering Off n-Alkanes, Cycloalkanes, and Six-Membered Rings: A Physical Interpretation. J Phys Chem B 2020; 124:7611-7624. [PMID: 32790389 PMCID: PMC7476039 DOI: 10.1021/acs.jpcb.0c03769] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/06/2020] [Indexed: 11/29/2022]
Abstract
Molecular liquids have long been known to undergo various distinct intermolecular motions, from fast librations and cage-rattling oscillations to slow orientational and translational diffusion. However, their resultant gigahertz to terahertz spectra are far from simple, appearing as broad shapeless bands that span many orders of magnitude of frequency, making meaningful interpretation troublesome. Ad hoc spectral line shape fitting has become a notoriously fine art in the field; a unified approach to handling such spectra is long overdue. Here we apply ultrafast optical Kerr-effect (OKE) spectroscopy to study the intermolecular dynamics of room-temperature n-alkanes, cycloalkanes, and six-carbon rings, as well as liquid methane and propane. This work provides stress tests and converges upon an experimentally robust model across simple molecular series and range of temperatures, providing a blueprint for the interpretation of the dynamics of van der Waals liquids. This will enable the interpretation of low-frequency spectra of more complex liquids.
Collapse
Affiliation(s)
- Andrew
J. Farrell
- School of Chemistry, University
of Glasgow, Glasgow G12 8QQ, United Kingdom
| | | | | | - Klaas Wynne
- School of Chemistry, University
of Glasgow, Glasgow G12 8QQ, United Kingdom
| |
Collapse
|
13
|
Andresen M, Schöngen D, Kleiner I, Schwell M, Stahl W, Nguyen HVL. Internal Rotation of the Acetyl Methyl Group in Methyl Alkyl Ketones: The Microwave Spectrum of Octan‐2‐one. Chemphyschem 2020; 21:2206-2216. [DOI: 10.1002/cphc.202000522] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/13/2020] [Indexed: 11/06/2022]
Affiliation(s)
- Maike Andresen
- Institute of Physical Chemistry RWTH Aachen University Landoltweg 2 52074 Aachen Germany
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA) CNRS UMR Université Paris-Est Créteil Université de Paris Institute Pierre Simon Laplace 61 avenue du Général de Gaulle 94010 Créteil France
| | - Damian Schöngen
- Institute of Physical Chemistry RWTH Aachen University Landoltweg 2 52074 Aachen Germany
| | - Isabelle Kleiner
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA) CNRS UMR Université Paris-Est Créteil Université de Paris Institute Pierre Simon Laplace 61 avenue du Général de Gaulle 94010 Créteil France
| | - Martin Schwell
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA) CNRS UMR Université Paris-Est Créteil Université de Paris Institute Pierre Simon Laplace 61 avenue du Général de Gaulle 94010 Créteil France
| | - Wolfgang Stahl
- Institute of Physical Chemistry RWTH Aachen University Landoltweg 2 52074 Aachen Germany
| | - Ha Vinh Lam Nguyen
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA) CNRS UMR Université Paris-Est Créteil Université de Paris Institute Pierre Simon Laplace 61 avenue du Général de Gaulle 94010 Créteil France
| |
Collapse
|
14
|
Baş EE, Karahan S, Köstereli Z, Haktanır M, Aviyente V. Pyrolysis of Alkanes: A Computational Approach. J Phys Chem A 2020; 124:5700-5708. [PMID: 32583668 DOI: 10.1021/acs.jpca.0c02858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, we investigate the kinetic and thermodynamic aspects of thermal cracking reactions of short paraffin chains by density functional theory (DFT) methods. The thermal cracking reactions have been modeled for a series of shorter unbranched alkanes at 673 K by following a free-radical mechanism. Benchmark calculations have been carried out with different functionals (B3LYP, M06-2X, PBE0, BMK, B3PW91) and basis sets (6-31G(d,p), 6-311+G(d,p)) to determine the most suitable DFT method, and the results were compared to the available experimental data. Computations were also performed at the CBS-QB3 level to evaluate the accuracy of the DFT method. The thermodynamic and kinetic properties of the initiation, hydrogen atom transfer (HAT), and decomposition (β-scission) reactions are intensely discussed to better understand the trends in product distributions at high temperatures. Evans-Polanyi (EP) relations have been used to build a linear relationship between the enthalpy of reactions and their activation energies; this process may be useful for the determination of the kinetic parameters of longer paraffin chains as well. Finally, the preexponential factors of short-chain paraffin have been calculated and classified based on the identity of the radicalic products. The latter, together with the activation energies derived from the EP relations can be used safely for the prediction of the rate constants for long paraffin chains.
Collapse
Affiliation(s)
- Ekin Esme Baş
- Faculty of Arts and Sciences, Department of Chemistry, Bogazici University, Bebek, 34342 Istanbul, Turkey
| | - Seda Karahan
- Turkish Petroleum Refineries Co. (TÜPRAŞ) R&D Center, 41790 Korfez, Kocaeli, Turkey
| | - Ziya Köstereli
- Turkish Petroleum Refineries Co. (TÜPRAŞ) R&D Center, 41790 Korfez, Kocaeli, Turkey
| | - Mert Haktanır
- Turkish Petroleum Refineries Co. (TÜPRAŞ) R&D Center, 41790 Korfez, Kocaeli, Turkey
| | - Viktorya Aviyente
- Faculty of Arts and Sciences, Department of Chemistry, Bogazici University, Bebek, 34342 Istanbul, Turkey
| |
Collapse
|
15
|
Perera A, Bartlett RJ, Sanders BA, Lotrich VF, Byrd JN. Advanced concepts in electronic structure (ACES) software programs. J Chem Phys 2020; 152:184105. [DOI: 10.1063/5.0002581] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Ajith Perera
- Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, Florida 32605, USA
| | - Rodney J. Bartlett
- Quantum Theory Project, Department of Chemistry, University of Florida, Gainesville, Florida 32605, USA
| | - Beverly A. Sanders
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida 32605, USA
| | | | | |
Collapse
|
16
|
Štejfa V, Fulem M, Růžička K. First-principles calculation of ideal-gas thermodynamic properties of long-chain molecules by R1SM approach—Application to n-alkanes. J Chem Phys 2019; 150:224101. [DOI: 10.1063/1.5093767] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Vojtěch Štejfa
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Michal Fulem
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| | - Květoslav Růžička
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague 6, Czech Republic
| |
Collapse
|
17
|
Pinski P, Neese F. Analytical gradient for the domain-based local pair natural orbital second order Møller-Plesset perturbation theory method (DLPNO-MP2). J Chem Phys 2019; 150:164102. [DOI: 10.1063/1.5086544] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Peter Pinski
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
18
|
Grineva OV. How do halogen atoms influence the competition between all-trans and hairpin conformers of unbranched alkanes? Struct Chem 2019. [DOI: 10.1007/s11224-019-1281-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
19
|
Dral PO, Wu X, Thiel W. Semiempirical Quantum-Chemical Methods with Orthogonalization and Dispersion Corrections. J Chem Theory Comput 2019; 15:1743-1760. [PMID: 30735388 PMCID: PMC6416713 DOI: 10.1021/acs.jctc.8b01265] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Indexed: 12/31/2022]
Abstract
We present two new semiempirical quantum-chemical methods with orthogonalization and dispersion corrections: ODM2 and ODM3 (ODM x). They employ the same electronic structure model as the OM2 and OM3 (OM x) methods, respectively. In addition, they include Grimme's dispersion correction D3 with Becke-Johnson damping and three-body corrections E ABC for Axilrod-Teller-Muto dispersion interactions as integral parts. Heats of formation are determined by adding explicitly computed zero-point vibrational energy and thermal corrections, in contrast to standard MNDO-type and OM x methods. We report ODM x parameters for hydrogen, carbon, nitrogen, oxygen, and fluorine that are optimized with regard to a wide range of carefully chosen state-of-the-art reference data. Extensive benchmarks show that the ODM x methods generally perform better than the available MNDO-type and OM x methods for ground-state and excited-state properties, while they describe noncovalent interactions with similar accuracy as OM x methods with a posteriori dispersion corrections.
Collapse
Affiliation(s)
- Pavlo O. Dral
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Xin Wu
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
20
|
Bumpus JA. Gas-Phase Heat of Formation Values for Buckminsterfullerene (C 60), C70 Fullerene (C 70), Corannulene, Coronene, Sumanene, and Other Polycyclic Aromatic Hydrocarbons Calculated Using Density Functional Theory (M06 2X) Coupled with a Versatile Inexpensive Group-Equivalent Approach. J Phys Chem A 2018; 122:6615-6632. [PMID: 30070846 DOI: 10.1021/acs.jpca.8b03321] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A straightforward procedure using density functional theory (M06 2X) coupled with a group-equivalent approach is described that was used to calculate gas-phase heat of formation (Δf H°g,298) values for buckminsterfullerene (C60), C70 fullerene (C70), corannulene, coronene, and sumanene. This procedure was also used to calculate exceptionally accurate Δf H°g,298 values for a variety of single-ring aromatic and 2-7 ring polycyclic aromatic hydrocarbons (PAHs) as well as a large selection of other hydrocarbons and phenols. The approach described herein is internally consistent, and results for C60, C70, corannulene, coronene, and sumanene are in very close agreement with results reported by others who used higher-level computational theory. Statistical analysis of a test set containing benzene and 18 two to seven ring PAHs demonstrated that by using this approach a mean absolute deviation (MAD) and a root-mean-square deviation (RMSD) of 0.8 and 1.3 kJ/mol, respectively, were achieved for reference/experimental Δf H°g,298 values versus calculated/predicted Δf H°g,298 values. For statistical analysis of a larger test set containing 235 aromatic and aliphatic hydrocarbons and phenols, a MAD and a RMSD of 1.2 and 1.9 kJ/mol, respectively, were achieved for reference/experimental Δf H°g,298 values versus calculated/predicted Δf H°g,298 values.
Collapse
Affiliation(s)
- John A Bumpus
- Department of Chemistry and Biochemistry , University of Northern Iowa , Cedar Falls , Iowa 50614 , United States
| |
Collapse
|
21
|
Radiom M, Maroni P, Wesolowski TA. Size extensivity of elastic properties of alkane fragments. J Mol Model 2018; 24:36. [PMID: 29313112 PMCID: PMC5758687 DOI: 10.1007/s00894-017-3572-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/14/2017] [Indexed: 12/01/2022]
Abstract
Using MP2, CCSD, and B3LYP methods of computational chemistry, we show length dependence in the intrinsic elastic properties of short alkane fragments. For isolated alkane fragments of finite length in the gas phase and zero temperature, the intrinsic elasticity constants are found to vary with the number of carbon atoms and its parity. From extrapolation of the elasticity constants calculations to infinite chain length, and by comparing with in-situ elasticity constant of single poly(ethylene) molecule obtained with atomic force microscopy, we estimate the softening effect of environment on the extension response of the polymer.
Collapse
Affiliation(s)
- Milad Radiom
- Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, 1205, Geneva, Switzerland.
- School of Chemical Science and Engineering, KTH Royal Institute of Technology, Drottning Kristinas väg 51, 10044, Stockholm, Sweden.
| | - Plinio Maroni
- Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, 1205, Geneva, Switzerland
| | - Tomasz A Wesolowski
- Department of Physical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, 1205, Geneva, Switzerland
| |
Collapse
|
22
|
van Gunsteren WF, Daura X, Hansen N, Mark AE, Oostenbrink C, Riniker S, Smith LJ. Validation of Molecular Simulation: An Overview of Issues. Angew Chem Int Ed Engl 2017; 57:884-902. [PMID: 28682472 DOI: 10.1002/anie.201702945] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Indexed: 12/14/2022]
Abstract
Computer simulation of molecular systems enables structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic, or supra-molecular level. To interpret results of such simulations appropriately, the quality of the calculated properties must be evaluated. This depends on the way the simulations are performed and on the way they are validated by comparison to values Qexp of experimentally observable quantities Q. One must consider 1) the accuracy of Qexp , 2) the accuracy of the function Q(rN ) used to calculate a Q-value based on a molecular configuration rN of N particles, 3) the sensitivity of the function Q(rN ) to the configuration rN , 4) the relative time scales of the simulation and experiment, 5) the degree to which the calculated and experimental properties are equivalent, and 6) the degree to which the system simulated matches the experimental conditions. Experimental data is limited in scope and generally corresponds to averages over both time and space. A critical analysis of the various factors influencing the apparent degree of (dis)agreement between simulations and experiment is presented and illustrated using examples from the literature. What can be done to enhance the validation of molecular simulation is also discussed.
Collapse
Affiliation(s)
- Wilfred F van Gunsteren
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine, Universitat Autonoma de Barcelona, UAB, 08193, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies, ICREA, 08010, Barcelona, Spain
| | - Niels Hansen
- Institute of Thermodynamics and Thermal Process Engineering, University of Stuttgart, Pfaffenwaldring 9, 70569, Stuttgart, Germany
| | - Alan E Mark
- School of Chemistry and Molecular Biosciences, University of Queensland, St. Lucia, QLD 4072, Australia
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Sereina Riniker
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, ETH, 8093, Zurich, Switzerland
| | - Lorna J Smith
- Department of Chemistry, Inorganic Chemistry, Laboratory, University of Oxford, South Parks Road, Oxford, OX1 3QR, UK
| |
Collapse
|
23
|
van Gunsteren WF, Daura X, Hansen N, Mark AE, Oostenbrink C, Riniker S, Smith LJ. Validierung von molekularen Simulationen: eine Übersicht verschiedener Aspekte. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702945] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Wilfred F. van Gunsteren
- Laboratorium für Physikalische Chemie; Eidgenössische Technische Hochschule Zürich; 8093 Zürich Schweiz
| | - Xavier Daura
- Institute of Biotechnology and Biomedicine; Universitat Autònoma de Barcelona; Spanien
- Catalan Institution for Research and Advanced Studies, ICREA; Barcelona Spanien
| | - Niels Hansen
- Institut für Technische Thermodynamik und Thermische Verfahrenstechnik; Universität Stuttgart; Deutschland
| | - Alan E. Mark
- School of Chemistry and Molecular Biosciences; University of Queensland; St. Lucia Australien
| | - Chris Oostenbrink
- Institut für Molekulare Modellierung und Simulation; Universität für Bodenkultur Wien; Österreich
| | - Sereina Riniker
- Laboratorium für Physikalische Chemie; Eidgenössische Technische Hochschule Zürich; 8093 Zürich Schweiz
| | - Lorna J. Smith
- Inorganic Chemistry Laboratory; Department of Chemistry; University of Oxford; Großbritannien
| |
Collapse
|
24
|
Margraf JT, Perera A, Lutz JJ, Bartlett RJ. Single-reference coupled cluster theory for multi-reference problems. J Chem Phys 2017; 147:184101. [DOI: 10.1063/1.5003128] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Johannes T. Margraf
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | - Ajith Perera
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | - Jesse J. Lutz
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | - Rodney J. Bartlett
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| |
Collapse
|
25
|
Barkley DA, Jiang N, Sen M, Endoh MK, Rudick JG, Koga T, Zhang Y, Gang O, Yuan G, Satija SK, Kawaguchi D, Tanaka K, Karim A. Chain Conformation near the Buried Interface in Nanoparticle-Stabilized Polymer Thin Films. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b01187] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
| | | | | | | | | | | | | | - Oleg Gang
- Department
of Chemical Engineering and Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
| | - Guangcui Yuan
- Center for
Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | - Sushil K. Satija
- Center for
Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
| | | | | | - Alamgir Karim
- College of
Polymer Science and Polymer Engineering, The University of Akron, Akron, Ohio 44325-0301, United States
| |
Collapse
|
26
|
Mata RA, Suhm MA. Benchmarking Quantum Chemical Methods: Are We Heading in the Right Direction? Angew Chem Int Ed Engl 2017; 56:11011-11018. [PMID: 28452424 PMCID: PMC5582598 DOI: 10.1002/anie.201611308] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/20/2016] [Indexed: 11/15/2022]
Abstract
Theoreticians and experimentalists should work together more closely to establish reliable rankings and benchmarks for quantum chemical methods. Comparison to carefully designed experimental benchmark data should be a priority. Guidelines to improve the situation for experiments and calculations are proposed.
Collapse
Affiliation(s)
- Ricardo A. Mata
- Institut für Physikalische ChemieUniversität GöttingenTammannstrasse 637077GöttingenGermany
| | - Martin A. Suhm
- Institut für Physikalische ChemieUniversität GöttingenTammannstrasse 637077GöttingenGermany
| |
Collapse
|
27
|
Truong K, Weger LB, Stahl W, Mouhib H. Favored Conformations of Carbonyl Compounds: A Structural Study ofn‐Octanal. Chemphyschem 2017; 18:2631-2636. [DOI: 10.1002/cphc.201700341] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 04/28/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Khai‐Nghi Truong
- Institute of Physical ChemistryRWTH Aachen University Landoltweg 2 52056 Aachen Germany
- Institute of Inorganic ChemistryRWTH Aachen University Landoltweg 1 52074 Aachen Germany
| | - Lindsey B. Weger
- Institute of Physical ChemistryRWTH Aachen University Landoltweg 2 52056 Aachen Germany
- Institute for Advanced Sustainability Studies, IASS Berliner Strasse 130 14467 Potsdam Germany
| | - Wolfgang Stahl
- Institute of Physical ChemistryRWTH Aachen University Landoltweg 2 52056 Aachen Germany
| | - Halima Mouhib
- Université Paris-EstLaboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS 5 bd Descartes 77454 Marne-la-Vallée France
| |
Collapse
|
28
|
Mata RA, Suhm MA. Quantenchemische Methoden im Leistungsvergleich: Stimmt die Richtung noch? Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611308] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Ricardo A. Mata
- Institut für Physikalische Chemie; Universität Göttingen; Tammannstraße 6 37077 Göttingen Deutschland
| | - Martin A. Suhm
- Institut für Physikalische Chemie; Universität Göttingen; Tammannstraße 6 37077 Göttingen Deutschland
| |
Collapse
|
29
|
Kirschner KN, Heiden W, Reith D. Relative electronic and free energies of octane's unique conformations. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1262076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Karl N. Kirschner
- Department of Computer Science, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany
- Institute of Visual Computing, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany
| | - Wolfgang Heiden
- Department of Computer Science, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany
- Institute of Visual Computing, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany
| | - Dirk Reith
- Institute of Visual Computing, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany
- Department of Electrical Engineering, Mechanical Engineering and Technical Journalism, Bonn-Rhein-Sieg University of Applied Sciences, Sankt Augustin, Germany
| |
Collapse
|
30
|
Silva Lopez C, Nieto Faza O, De Proft F, Kolocouris A. Assessing the attractive/repulsive force balance in axial cyclohexane C-Hax···Yaxcontacts: A combined computational analysis in monosubstituted cyclohexanes. J Comput Chem 2016; 37:2647-2658. [DOI: 10.1002/jcc.24496] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 08/26/2016] [Accepted: 09/01/2016] [Indexed: 02/03/2023]
Affiliation(s)
- Carlos Silva Lopez
- Departamento de Química Orgánica; Facultade de Química, Universidade de Vigo; Vigo, 63 Spain310
| | - Olalla Nieto Faza
- Departamento de Química Orgánica; Facultade de Química, Universidade de Vigo; Vigo, 63 Spain310
| | - Frank De Proft
- Eenheid Algemene Chemie, Faculteit Wetenschappen; Vrije Universiteit Brussel; Pleinlaan 2 Brussels B-1050 Belgium
| | - Antonios Kolocouris
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry; National and Kapodistrian University of Athens; Panepistimioupolis-Zografou Athens 15771 Greece
| |
Collapse
|
31
|
Byrd JN, Lutz JJ, Jin Y, Ranasinghe DS, Montgomery JA, Perera A, Duan XF, Burggraf LW, Sanders BA, Bartlett RJ. Predictive coupled-cluster isomer orderings for some SinCm(m,n≤ 12) clusters: A pragmatic comparison between DFT and complete basis limit coupled-cluster benchmarks. J Chem Phys 2016; 145:024312. [DOI: 10.1063/1.4955196] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jason N. Byrd
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
- ENSCO, Inc., 4849 North Wickham Road, Melbourne, Florida 32940, USA
| | - Jesse J. Lutz
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | - Yifan Jin
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | | | - John A. Montgomery
- Department of Physics, University of Connecticut, Storrs, Connecticut 06269, USA
| | - Ajith Perera
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| | - Xiaofeng F. Duan
- Air Force Institute of Technology, Wright-Patterson Air Force Base, Ohio 45433, USA
- Air Force Research Laboratory DoD Supercomputing Resource Center, Wright-Patterson Air Force Base, Ohio 45433, USA
| | - Larry W. Burggraf
- Air Force Institute of Technology, Wright-Patterson Air Force Base, Ohio 45433, USA
| | - Beverly A. Sanders
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida 32611, USA
| | - Rodney J. Bartlett
- Quantum Theory Project, University of Florida, Gainesville, Florida 32611, USA
| |
Collapse
|
32
|
Dral P, Wu X, Spörkel L, Koslowski A, Thiel W. Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Benchmarks for Ground-State Properties. J Chem Theory Comput 2016; 12:1097-120. [PMID: 26771261 PMCID: PMC4785506 DOI: 10.1021/acs.jctc.5b01047] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Indexed: 11/30/2022]
Abstract
The semiempirical orthogonalization-corrected OMx methods (OM1, OM2, and OM3) go beyond the standard MNDO model by including additional interactions in the electronic structure calculation. When augmented with empirical dispersion corrections, the resulting OMx-Dn approaches offer a fast and robust treatment of noncovalent interactions. Here we evaluate the performance of the OMx and OMx-Dn methods for a variety of ground-state properties using a large and diverse collection of benchmark sets from the literature, with a total of 13035 original and derived reference data. Extensive comparisons are made with the results from established semiempirical methods (MNDO, AM1, PM3, PM6, and PM7) that also use the NDDO (neglect of diatomic differential overlap) integral approximation. Statistical evaluations show that the OMx and OMx-Dn methods outperform the other methods for most of the benchmark sets.
Collapse
Affiliation(s)
- Pavlo
O. Dral
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
| | - Xin Wu
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
| | - Lasse Spörkel
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
| | - Axel Koslowski
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
| |
Collapse
|
33
|
Pastorczak E, Prlj A, Gonthier JF, Corminboeuf C. Intramolecular symmetry-adapted perturbation theory with a single-determinant wavefunction. J Chem Phys 2015; 143:224107. [DOI: 10.1063/1.4936830] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ewa Pastorczak
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Antonio Prlj
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Jérôme F. Gonthier
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Clémence Corminboeuf
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| |
Collapse
|
34
|
Jeong C, Douglas JF. Mass dependence of the activation enthalpy and entropy of unentangled linear alkane chains. J Chem Phys 2015; 143:144905. [DOI: 10.1063/1.4932601] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
|
35
|
Thakkar AJ, Wu T. How well do static electronic dipole polarizabilities from gas-phase experiments compare with density functional and MP2 computations? J Chem Phys 2015; 143:144302. [DOI: 10.1063/1.4932594] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
36
|
Santamaria R, Jones K, Arroyo M, González-García T. Polymer folding via external potentials in ab-initio calculations. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
37
|
Coupled cluster geometries and energies of C20 carbon cluster isomers – A new benchmark study. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.04.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
38
|
Jankovič L, Kronek J, Madejová J, Hronský V. (9,10‐Dihydroxyoctadecyl)ammonium: A Structurally Unique Class of Clay Intercalable Surfactants. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Luboš Jankovič
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84536 Bratislava, Slovakia, http://www.uach.sav.sk/
| | - Juraj Kronek
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 84541 Bratislava, Slovakia
| | - Jana Madejová
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84536 Bratislava, Slovakia, http://www.uach.sav.sk/
| | - Viktor Hronský
- Department of Physics, Faculty of Electrical Engineering and Informatics, Technical University of Košice, Park Komenského 2, 04200 Košice, Slovakia
| |
Collapse
|
39
|
Liakos DG, Neese F. Domain Based Pair Natural Orbital Coupled Cluster Studies on Linear and Folded Alkane Chains. J Chem Theory Comput 2015; 11:2137-43. [DOI: 10.1021/acs.jctc.5b00265] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dimitrios G. Liakos
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 32-34, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 32-34, 45470 Mülheim an der Ruhr, Germany
| |
Collapse
|
40
|
Rojas L, Ruette F, Peraza A, Castellano O, Soscún H. Relationship between unbranched alkane dimer interaction energies using different theoretical methods and correlations with thermodynamic properties. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.02.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
41
|
Mansbach RA, Ferguson AL. Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics. J Chem Phys 2015; 142:105101. [DOI: 10.1063/1.4914144] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
|
42
|
Persch E, Dumele O, Diederich F. Molekulare Erkennung in chemischen und biologischen Systemen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408487] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
43
|
Persch E, Dumele O, Diederich F. Molecular recognition in chemical and biological systems. Angew Chem Int Ed Engl 2015; 54:3290-327. [PMID: 25630692 DOI: 10.1002/anie.201408487] [Citation(s) in RCA: 419] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 12/13/2022]
Abstract
Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.
Collapse
Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
| | | | | |
Collapse
|
44
|
Lüttschwager NOB, Suhm MA. Stretching and folding of 2-nanometer hydrocarbon rods. SOFT MATTER 2014; 10:4885-4901. [PMID: 24866111 DOI: 10.1039/c4sm00508b] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Linear alkanes CnH2n+2 in vacuum isolation are finite models for an infinite polyethylene chain. Using spontaneous Raman scattering in supersonic jet expansions for n = 13-21 in different spectral ranges, we determine the minimal chain length nh for the cohesion-driven folding of the preferred extended all-trans conformation into a hairpin structure. We treat fully stretched all-trans alkanes as molecular "nanorods" and derive Young's modulus E for the stretching of an isolated single-strand polyethylene fibre by extrapolating the longitudinal acoustic mode to infinite chain length. Two key quality parameters for accurate intra- and intermolecular force fields of hydrocarbons (nh = 18 ± 1, E = 305 ± 5 GPa) are thus derived with high accuracy from experimental spectroscopy.
Collapse
Affiliation(s)
- Nils O B Lüttschwager
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany.
| | | |
Collapse
|
45
|
Darensbourg DJ, Yeung AD. A concise review of computational studies of the carbon dioxide–epoxide copolymerization reactions. Polym Chem 2014. [DOI: 10.1039/c4py00299g] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The production of polycarbonates from carbon dioxide and epoxides is an important route by which waste CO2 is converted into useful products. This review surveys the use of computational chemistry toward understanding this reaction.
Collapse
|