1
|
Pérez-Barcia Á, Cárdenas G, Nogueira JJ, Mandado M. Effect of the QM Size, Basis Set, and Polarization on QM/MM Interaction Energy Decomposition Analysis. J Chem Inf Model 2023; 63:882-897. [PMID: 36661314 PMCID: PMC9930123 DOI: 10.1021/acs.jcim.2c01184] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Herein, an Energy Decomposition Analysis (EDA) scheme extended to the framework of QM/MM calculations in the context of electrostatic embeddings (QM/MM-EDA) including atomic charges and dipoles is applied to assess the effect of the QM region size on the convergence of the different interaction energy components, namely, electrostatic, Pauli, and polarization, for cationic, anionic, and neutral systems interacting with a strong polar environment (water). Significant improvements are found when the bulk solvent environment is described by a MM potential in the EDA scheme as compared to pure QM calculations that neglect bulk solvation. The predominant electrostatic interaction requires sizable QM regions. The results reported here show that it is necessary to include a surprisingly large number of water molecules in the QM region to obtain converged values for this energy term, contrary to most cluster models often employed in the literature. Both the improvement of the QM wave function by means of a larger basis set and the introduction of polarization into the MM region through a polarizable force field do not translate to a faster convergence with the QM region size, but they lead to better results for the different interaction energy components. The results obtained in this work provide insight into the effect of each energy component on the convergence of the solute-solvent interaction energy with the QM region size. This information can be used to improve the MM FFs and embedding schemes employed in QM/MM calculations of solvated systems.
Collapse
Affiliation(s)
- Álvaro Pérez-Barcia
- Department
of Physical Chemistry, University of Vigo, Lagoas-Marcosende s\n, ES-36310-Vigo, Galicia, Spain
| | - Gustavo Cárdenas
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049, Madrid, Spain
| | - Juan J. Nogueira
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049, Madrid, Spain,Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049Madrid, Spain,E-mail:
| | - Marcos Mandado
- Department
of Physical Chemistry, University of Vigo, Lagoas-Marcosende s\n, ES-36310-Vigo, Galicia, Spain,E-mail:
| |
Collapse
|
2
|
Kristoffersen HH. Modeling electrochemical proton adsorption at constant potential with explicit charging. ChemCatChem 2022. [DOI: 10.1002/cctc.202200826] [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)
- Henrik H. Kristoffersen
- University of Copenhagen: Kobenhavns Universitet Department of Chemistry 2100 København Ø DENMARK
| |
Collapse
|
3
|
Zhao L, Zhang J. Intermolecular interaction of diamine-diol binary system: A mini-review. Adv Colloid Interface Sci 2022; 304:102662. [PMID: 35453067 DOI: 10.1016/j.cis.2022.102662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 11/01/2022]
Abstract
The highly selective chemical reaction of carbon dioxide with organic amines is considered to a mature technology and a feasible initial path for carbon capture. In order to solve the disadvantages of high volatility, equipment corrosion and high energy consumption of traditional organic amines, amine alcohol "mixture based" solution has been developed and showed excellent carbon dioxide absorption capacity, which is due to the positive effect of intermolecular interaction in amine alcohol "mixture based" solution system on thermodynamic properties. However, the influencing factors of the intermolecular force in multicomponent solution system are complex, including the chemical, physical, structural effects. Therefore, it is necessary to comprehensively use a variety of characterization methods to systematically understand the form of intermolecular interaction in multicomponent solution system. This review systematically discusses the determination of intermolecular interactions in diamine-diol multicomponent solutions by three mainstream research methods, theoretical calculation method, spectral method, and thermodynamic method, aiming to provide a theoretical reference for the industrial production, the supplement to experimental data, and construction and understanding of theoretical models of multicomponent solution system.
Collapse
|
4
|
Lomboy AJV, Topper RQ. Nonuniform Proton Transfer and Strong Hydrogen Bonding within Cation, Anion, and Neutral Clusters of Ammonia and Hydrogen Fluoride. J Phys Chem A 2021; 125:2546-2557. [PMID: 33733769 DOI: 10.1021/acs.jpca.1c00732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structural studies of ammonium halide nanoparticles can help to reveal fundamental information about the detailed nature of intermolecular forces. This study focuses on small ammonium fluoride clusters, which exhibit complex behavior in comparison to other ammonium halide clusters due to the weak acidity and strong hydrogen-bonding ability of HF. Calculations of optimized structures and binding energies are presented for cation, anion, and neutral clusters using MP2, CCSD(T), FNO-CCSD(T), ωB97M-V, and MN15 methods. The extent to which proton transfer occurs between two given cluster components was quantified using a dimensionless proton-transfer parameter (ξPT), leading to a classification of different types of hydrogen bonds within the clusters. Whereas the neutral clusters exhibit a complex transition from ordinary hydrogen bonding to a combination of shared-proton hydrogen bonds and complete proton transfers, the anion and cation systems exhibit a rapid transition toward complete proton transfer from HF to NH3, with incomplete proton transfer observed only in the smallest anion and cation clusters. Ionic interaction energies of these clusters were also computed and found to exhibit trends which can be interpreted by the size-dependent behavior of ξPT. This work extends our understanding of the size-dependent trends in intermolecular forces which govern the formation of anhydrous ammonium halide clusters as well as the relationship between strong hydrogen bonding and proton transfer.
Collapse
Affiliation(s)
- Anna Joselle V Lomboy
- Department of Chemistry and Department of Chemical Engineering, The Cooper Union for the Advancement of Science and Art, New York, New York 10003, United States
| | - Robert Q Topper
- Department of Chemistry, The Cooper Union for the Advancement of Science and Art, New York, New York 10003, United States
| |
Collapse
|
5
|
Jiang LL, Song YF, Liu WL, Wu HL, Li XY, Yang YQ. Ultrafast characteristics of vibrational dynamics in tetrahydrofuran via femtosecond coherent anti-stokes Raman scattering. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2020.138256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
6
|
Mehta N, Goerigk L. Assessing the Applicability of the Geometric Counterpoise Correction in B2PLYP/Double-ζ Calculations for Thermochemistry, Kinetics, and Noncovalent Interactions. Aust J Chem 2021. [DOI: 10.1071/ch21133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We present a proof-of-concept study of the suitability of Kruse and Grimme’s geometric counterpoise correction (gCP) for basis set superposition errors (BSSEs) in double-hybrid density functional calculations with a double-ζ basis set. The gCP approach only requires geometrical information as an input and no orbital/density information is needed. Therefore, this correction is practically free of any additional cost. gCP is trained against the Boys and Bernardi counterpoise correction across a set of 528 noncovalently bound dimers. We investigate the suitability of the approach for the B2PLYP/def2-SVP level of theory, and reveal error compensation effects—missing London dispersion and the BSSE—associated with B2PLYP/def2-SVP calculations, and present B2PLYP-gCP-D3(BJ)/def2-SVP with the reparametrised DFT-D3(BJ) and gCP corrections as a more balanced alternative. Benchmarking results on the S66x8 benchmark set for noncovalent interactions and the GMTKN55 database for main-group thermochemistry, kinetics, and noncovalent interactions show a statistical improvement of the B2PLYP-gCP-D3(BJ) scheme over plain B2PLYP and B2PLYP-D3(BJ). B2PLYP-D3(BJ) shows significant overestimation of interaction energies, barrier heights with larger deviations from the reference values, and wrong relative stabilities in conformers, all of which can be associated with BSSE. We find that the gCP-corrected method represents a significant improvement over B2PLYP-D3(BJ), particularly for intramolecular noncovalent interactions. These findings encourage future developments of efficient double-hybrid DFT strategies that can be applied when double-hybrid calculations with large basis sets are not feasible due to system size.
Collapse
|
7
|
Grein F. CH4O2, NH3O2, H2O O2 and HF O2 triplet complexes. Ab initio studies and comparisons. From van der Waals to hydrogen bonding. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112834] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
8
|
On the Use of Popular Basis Sets: Impact of the Intramolecular Basis Set Superposition Error. Molecules 2019; 24:molecules24203810. [PMID: 31652663 PMCID: PMC6832644 DOI: 10.3390/molecules24203810] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 11/16/2022] Open
Abstract
The magnitude of intramolecular basis set superposition error (BSSE) is revealed via computing systematic trends in molecular properties. This type of error is largely neglected in the study of the chemical properties of small molecules and it has historically been analyzed just in the study of large molecules and processes dominated by non-covalent interactions (typically dimerization or molecular complexation and recognition events). In this work we try to provide proof of the broader prevalence of this error, which permeates all types of electronic structure calculations, particularly when employing insufficiently large basis sets.
Collapse
|
9
|
Performance of polarization-consistent vs. correlation-consistent basis sets for CCSD(T) prediction of water dimer interaction energy. J Mol Model 2019; 25:313. [DOI: 10.1007/s00894-019-4200-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2019] [Accepted: 08/30/2019] [Indexed: 10/26/2022]
Abstract
Abstract
Detailed study of Jensen’s polarization-consistent vs. Dunning’s correlation-consistent basis set families performance on the extrapolation of raw and counterpoise-corrected interaction energies of water dimer using coupled cluster with single, double, and perturbative correction for connected triple excitations (CCSD(T)) in the complete basis set (CBS) limit are reported. Both 3-parameter exponential and 2-parameter inverse-power fits vs. the cardinal number of basis set, as well as the number of basis functions were analyzed and compared with one of the most extensive CCSD(T) results reported recently. The obtained results for both Jensen- and Dunning-type basis sets underestimate raw interaction energy by less than 0.136 kcal/mol with respect to the reference value of − 4.98065 kcal/mol. The use of counterpoise correction further improves (closer to the reference value) interaction energy. Asymptotic convergence of 3-parameter fitted interaction energy with respect to both cardinal number of basis set and the number of basis functions are closer to the reference value at the CBS limit than other fitting approaches considered here. Separate fits of Hartree-Fock and correlation interaction energy with 3-parameter formula additionally improved the results, and the smallest CBS deviation from the reference value is about 0.001 kcal/mol (underestimated) for CCSD(T)/aug-cc-pVXZ calculations. However, Jensen’s basis set underestimates such value to 0.012 kcal/mol. No improvement was observed for using the number of basis functions instead of cardinal number for fitting.
Collapse
|
10
|
Harabuchi Y, Tani R, De Silva N, Njegic B, Gordon MS, Taketsugu T. Anharmonic vibrational computations with a quartic force field for curvilinear coordinates. J Chem Phys 2019. [DOI: 10.1063/1.5096167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Yu Harabuchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Ryosuke Tani
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Nuwan De Silva
- Department of Physical and Biological Sciences, Western New England University, Springfield, Massachusetts 01119, USA
| | - Bosiljka Njegic
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA
| | - Tetsuya Taketsugu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
| |
Collapse
|
11
|
Zhang W, Fang C, Fang Y, Zhu F, Zhou Y, Liu H, Li W. Structure of aqueous cesium metaborate solutions by X-ray scattering and DFT calculation. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2017.12.099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
12
|
Analysis of polarization in hydrogen bonded complexes: An asymptotic projection approach. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.02.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
13
|
Lin C, Kumar M, Finney BA, Francisco JS. Intramolecular hydrogen bonding in malonaldehyde and its radical analogues. J Chem Phys 2017; 147:124309. [PMID: 28964036 DOI: 10.1063/1.4996563] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
High level Brueckner doubles with triples correction method-based ab initio calculations have been used to investigate the nature of intramolecular hydrogen bonding and intramolecular hydrogen atom transfer in cis-malonaldehyde (MA) and its radical analogues. The radicals considered here are the ones that correspond to the homolytic cleavage of C-H bonds in cis-MA. The results suggest that cis-MA and its radical analogues, cis-MARS, and cis-MARA, both exist in planar geometry. The calculated intramolecular O-H⋯O=C bond in cis-MA is shorter than that in the radical analogues. The intramolecular hydrogen bond in cis-MA is stronger than in its radicals by at least 3.0 kcal/mol. The stability of a cis-malonaldehyde radical correlates with the extent of electron spin delocalization; cis-MARA, in which the radical spin is more delocalized, is the most stable MA radical, whereas cis-MARS, in which the radical spin is strongly localized, is the least stable radical. The natural bond orbital analysis indicates that the intramolecular hydrogen bonding (O⋯H⋯O) in cis-malonaldehyde radicals is stabilized by the interaction between the lone pair orbitals of donor oxygen and the σ* orbital of acceptor O-H bond (n → σ*OH). The calculated barriers indicate that the intramolecular proton transfer in cis-MA involves 2.2 kcal/mol lower barrier than that in cis-MARS.
Collapse
Affiliation(s)
- Chen Lin
- Department of Chemistry and Department of Earth and Atmospheric Science, Purdue University, West Lafayette, Indiana 47907-1393, USA
| | - Manoj Kumar
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588-0321, USA
| | - Brian A Finney
- Department of Chemistry and Department of Earth and Atmospheric Science, Purdue University, West Lafayette, Indiana 47907-1393, USA
| | - Joseph S Francisco
- Department of Chemistry and Department of Earth and Atmospheric Science, Purdue University, West Lafayette, Indiana 47907-1393, USA
| |
Collapse
|
14
|
García-LLinás X, Bauzá A, Seth SK, Frontera A. Importance of R–CF3···O Tetrel Bonding Interactions in Biological Systems. J Phys Chem A 2017; 121:5371-5376. [DOI: 10.1021/acs.jpca.7b06052] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Xavier García-LLinás
- Department of Chemistry, Universitat de les Illes Balears, Crta. De Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain
| | - Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta. De Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain
| | - Saikat K. Seth
- Department of Chemistry, Universitat de les Illes Balears, Crta. De Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain
- Department of Physics, Jadavpur University, Kolkata 700032, India
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. De Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain
| |
Collapse
|
15
|
Witte J, Neaton JB, Head-Gordon M. Effective empirical corrections for basis set superposition error in the def2-SVPD basis: gCP and DFT-C. J Chem Phys 2017. [DOI: 10.1063/1.4986962] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
|
16
|
Witte J, Neaton JB, Head-Gordon M. Push it to the limit: Characterizing the convergence of common sequences of basis sets for intermolecular interactions as described by density functional theory. J Chem Phys 2017; 144:194306. [PMID: 27208948 DOI: 10.1063/1.4949536] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
With the aim of systematically characterizing the convergence of common families of basis sets such that general recommendations for basis sets can be made, we have tested a wide variety of basis sets against complete-basis binding energies across the S22 set of intermolecular interactions-noncovalent interactions of small and medium-sized molecules consisting of first- and second-row atoms-with three distinct density functional approximations: SPW92, a form of local-density approximation; B3LYP, a global hybrid generalized gradient approximation; and B97M-V, a meta-generalized gradient approximation with nonlocal correlation. We have found that it is remarkably difficult to reach the basis set limit; for the methods and systems examined, the most complete basis is Jensen's pc-4. The Dunning correlation-consistent sequence of basis sets converges slowly relative to the Jensen sequence. The Karlsruhe basis sets are quite cost effective, particularly when a correction for basis set superposition error is applied: counterpoise-corrected def2-SVPD binding energies are better than corresponding energies computed in comparably sized Dunning and Jensen bases, and on par with uncorrected results in basis sets 3-4 times larger. These trends are exhibited regardless of the level of density functional approximation employed. A sense of the magnitude of the intrinsic incompleteness error of each basis set not only provides a foundation for guiding basis set choice in future studies but also facilitates quantitative comparison of existing studies on similar types of systems.
Collapse
Affiliation(s)
- Jonathon Witte
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Jeffrey B Neaton
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| |
Collapse
|
17
|
Testing the CP-correction procedure with different DFT methods on H-bonding complexes of κ-carrabiose with water molecules. J Mol Model 2017; 23:31. [PMID: 28091888 DOI: 10.1007/s00894-016-3199-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/16/2016] [Indexed: 10/20/2022]
Abstract
Interaction of water molecules with κ-carrabiose disaccharide, within three H-bonding complexes, was investigated. Particular interest was focused on the way with which the BSSE correction has to be performed. Two strategies were used, either performing BSSE correction during or after optimization. For this aim, several DFT-functionals (hybrid GGA and hybrid meta-GGA) and 6-31 + G* basis set were considered. The results demonstrated the uselessness of including of BSSE-CP correction during optimization for all complexes. From a structural point of view, a proper H-bonding description was obtained using the PBE0 functional for all complexes. The basis set effect on the BSSE using B3LYP functional was also investigated. The reliability of B3LYP/6-31 + G** and B3LYP/6-31++G** models for the complexes involving one or two water molecules was reported while the use of B3LYP/6-311 + G** or B3LYP/6-311++G** levels was shown to be more appropriate for larger complexes equivalent to that involving three water molecules. CP-corrected interaction energies were demonstrated to be closer to CBS-4 M interaction energies than the uncorrected ones. Graphical abstract Functional and basis set effects on BSSE.
Collapse
|
18
|
Venkatakrishnan HA, Venkatakrishnan R, Pennathur AK, Pennathur G. Structure and simulation of a Zundel ion stabilized by 8-hydroxyquinoline-5, 7 disulphonic acid. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2016.02.096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
19
|
Lu N, Chung WC, Ley RM, Lin KY, Francisco JS, Negishi EI. Molecularly Tuning the Radicaloid N-H···O═C Hydrogen Bond. J Phys Chem A 2016; 120:1307-15. [PMID: 26855203 DOI: 10.1021/acs.jpca.6b00144] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Substituent effects on the open shell N-H···O═C hydrogen-bond has never been reported. This study examines how 12 functional groups composed of electron donating groups (EDG), halogen atoms and electron withdrawing groups (EWG) affect the N-H···O═C hydrogen-bond properties in a six-membered cyclic model system of O═C(Y)-CH═C(X)N-H. It is found that group effects on this open shell H-bonding system are significant and have predictive trends when X = H and Y is varied. When Y is an EDG, the N-H···O═C hydrogen-bond is strengthened; and when Y is an EWG, the bond is weakened; whereas the variation in electronic properties of X group do not exhibit a significant impact upon the hydrogen bond strength. The structural impact of the stronger N-H···O═C hydrogen-bond are (1) shorter H and O distance, r(H···O) and (2) a longer N-H bond length, r(NH). The stronger N-H···O═C hydrogen-bond also acts to pull the H and O in toward one another which has an effect on the bond angles. Our findings show that there is a linear relationship between hydrogen-bond angle and N-H···O═C hydrogen-bond energy in this unusual H-bonding system. In addition, there is a linear correlation of the r(H···O) and the hydrogen bond energy. A short r(H···O) distance corresponds to a large hydrogen bond energy when Y is varied. The observed trends and findings have been validated using three different methods (UB3LYP, M06-2X, and UMP2) with two different basis sets.
Collapse
Affiliation(s)
- Norman Lu
- Department of Chemistry, Purdue University , 1393 Brown Building, West Lafayette, Indiana 47907-1393, United States.,Institute of Organic and Polymeric Materials, National Taipei University of Technology , Taipei 106, Taiwan
| | - Wei-Cheng Chung
- Institute of Organic and Polymeric Materials, National Taipei University of Technology , Taipei 106, Taiwan
| | - Rebecca M Ley
- Department of Chemistry, Purdue University , 1393 Brown Building, West Lafayette, Indiana 47907-1393, United States
| | - Kwan-Yu Lin
- Institute of Organic and Polymeric Materials, National Taipei University of Technology , Taipei 106, Taiwan
| | - Joseph S Francisco
- Department of Chemistry, Purdue University , 1393 Brown Building, West Lafayette, Indiana 47907-1393, United States.,Department of Chemistry, University of Nebraska-Lincoln , Lincoln, Nebraska 68588, United States
| | - Ei-Ichi Negishi
- Department of Chemistry, Purdue University , 1393 Brown Building, West Lafayette, Indiana 47907-1393, United States
| |
Collapse
|
20
|
Fogarasi G, Szalay PG. Quantum chemical MP2 results on some hydrates of cytosine: binding sites, energies and the first hydration shell. Phys Chem Chem Phys 2015; 17:29880-90. [PMID: 26487481 DOI: 10.1039/c5cp04563k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A detailed quantum chemical investigation was undertaken to obtain the structure and energetics of cytosine hydrates Cyt·nH2O, with n = 1 to 7. The MP2(fc)/aug-cc-pVDZ level was used as the standard, with some DFT (B3LYP) and coupled cluster calculations, as well as calculations with the aug-cc-pVTZ basis set added for comparison. In a systematic search for microhydrated forms of cytosine, we have found that several structures have not yet been reported in the literature. The energies of different isomers, as well as binding energies are compared. When predicting the stability of a complex, we suggest using a scheme where the water molecules are extracted from a finite model of bulk water. Finally, based on energetic data, we suggest a rational definition of the first hydration shell; with this definition, it contains just six water molecules.
Collapse
Affiliation(s)
- Géza Fogarasi
- Institute of Chemistry, Eötvös University, P.O. Box 32, H-1518 Budapest, Hungary.
| | | |
Collapse
|
21
|
Alkorta I, Elguero J, Del Bene JE. Exploring the PX3:NCH and PX3:NH3 potential surfaces, with X = F, Cl, and Br. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.10.050] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
22
|
Park SS, Lee S, Won YS, Ahn YJ. Comparative investigation of polyhedral water cages of (H2O)n (n=20, 24, and 28) encaging CH4 and SF6 as guest molecules. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.07.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
23
|
A theoretical study of the thermodynamic and hydrogen-bond basicity of TEMPO radical and related nitroxides. Struct Chem 2014. [DOI: 10.1007/s11224-014-0484-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
24
|
Ramabhadran RO, Liu Y, Hua Y, Ciardi M, Flood AH, Raghavachari K. An overlooked yet ubiquitous fluoride congenitor: binding bifluoride in triazolophanes using computer-aided design. J Am Chem Soc 2014; 136:5078-89. [PMID: 24559019 DOI: 10.1021/ja500125r] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Despite its ubiquity during the binding and sensing of fluoride, the role of bifluoride (HF2(-)) and its binding properties are almost always overlooked. Here, we give one of the first examinations of bifluoride recognition in which we use computer-aided design to modify the cavity shape of triazolophanes to better match with HF2(-). Computational investigation indicates that HF2(-) and Cl(-) should have similar binding affinities to the parent triazolophane in the gas phase. Evaluation of the binding geometries revealed a preference for binding of the linear HF2(-) along the north-south axis with a smaller Boltzmann weighted population aligned east-west and all states being accessed rapidly through in-plane precessional rotations of the anion. While the (1)H NMR spectroscopy studies are consistent with the calculated structural aspects, binding affinities in solution were determined to be significantly smaller for the bifluoride than the chloride. Computed geometries suggested that a 20° tilting of the bifluoride (stemming from the cavity size) could account for the 25-fold difference between the two binding affinities, HF2(-) < Cl(-). Structural variations to the triazolophane's geometry and electronic modifications to the network of hydrogen bond donors were subsequently screened in a stepwise manner using density functional theory calculations to yield a final design that eliminates the tilting. Correspondingly, the bifluoride's binding affinity (K ∼ 10(6) M(-1)) increased and was also found to remain equal to chloride in the gas and solution phases. The new oblate cavity appeared to hold the HF2(-) in a single east-west arrangement. Our findings demonstrate the promising ability of computer-aided design to fine-tune the structural and electronic match in anion receptors as a means to control the arrangement and binding strength of a desired guest.
Collapse
Affiliation(s)
- Raghunath O Ramabhadran
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | | | | | | | | | | |
Collapse
|
25
|
Belikov VV, Bokhan DA, Trubnikov DN. Estimating the basis set superposition error in the CCSD(T)(F12) explicitly correlated method using the example of a water dimer. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2014. [DOI: 10.1134/s0036024414040037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
26
|
|
27
|
Tian QP, Wang YH, Shi WJ, song SQ, Tang HF. A theoretical investigation into the cooperativity effect between the H∙∙∙O and H∙∙∙F– interactions and electrostatic potential upon 1:2 (F–:N-(Hydroxymethyl)acetamide) ternary-system formation. J Mol Model 2013; 19:5171-85. [DOI: 10.1007/s00894-013-2011-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/11/2013] [Indexed: 01/16/2023]
|
28
|
Feng GR, Qi TY, Shi WJ, Yan YG, Guo YX. A B3LYP and MP2 theoretical investigation into the synergetic effect between the O/NH⋯O and O/NH⋯F− anionic hydrogen-bonding interactions in N-(Hydroxymethyl)acetamide complex with F−. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
29
|
TADI KIRANKUMAR, MOTGHARE RV. Computational and experimental studies on oxalic acid imprinted polymer. J CHEM SCI 2013. [DOI: 10.1007/s12039-013-0381-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
30
|
Borner A, Li Z, Levin DA. Development of a molecular-dynamics-based cluster-heat-capacity model for study of homogeneous condensation in supersonic water-vapor expansions. J Chem Phys 2013; 138:064302. [DOI: 10.1063/1.4790476] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
|
31
|
Huš M, Urbic T. Strength of hydrogen bonds of water depends on local environment. J Chem Phys 2012; 136:144305. [PMID: 22502516 DOI: 10.1063/1.3701616] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In-depth knowledge of water-water potential is important for devising and evaluating simple water models if they are to accurately describe water properties and reflect various solvation phenomena. Water-water potential depends upon inter-molecular distance, relative orientation of water molecules, and also local environment. When placed at a favorable distance in a favorable orientation, water molecules exhibit a particularly strong attractive interaction called hydrogen bond. Although hydrogen bond is very important for its effects on the elements of life, industrial applications, and bulk water properties, there is no scientific consensus on its true nature and origin. Using quantum-mechanical methods, hydrogen bond strength was calculated in different local environments. A simple empirical linear relationship was discovered between maximum hydrogen bond strength and the number of water molecules in the local environment. The local environment effect was shown to be considerable even on the second coordination shell. Additionally, a negative linear correlation was found between maximum hydrogen bond strength and the distance, at which it was observed. These results provide novel insights into the nature of hydrogen bonding.
Collapse
Affiliation(s)
- Matej Huš
- University of Ljubljana, Department of Chemistry and Chemical Engineering, Chair of Physical Chemistry, Aškerčeva 5, SI-1000 Ljubljana, Slovenia.
| | | |
Collapse
|
32
|
Belosludov RV, Mizuseki H, Souissi M, Kawazoe Y, Kudoh J, Subbotin OS, Adamova TP, Belosludov VR. An atomistic level description of guest molecule effect on the formation of hydrate crystal nuclei by ab initio calculations. J STRUCT CHEM+ 2012. [DOI: 10.1134/s0022476612040014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
33
|
High level theoretical study of binding and of the potential energy surface in benzene–hydride system. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.03.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
34
|
Golec B, Mucha M, Mielke Z. Complexation of formaldoxime with water. Infrared matrix isolation and theoretical studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 86:461-466. [PMID: 22127136 DOI: 10.1016/j.saa.2011.10.069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 10/23/2011] [Accepted: 10/31/2011] [Indexed: 05/31/2023]
Abstract
The 1:1, 1:2 and 2:1 formaldoxime-water complexes isolated in the argon matrices have been studied by help of FTIR spectroscopy and MP2/6-311++G(2d,2p) method. The calculations predicted the stability of the three CH(2)NOH···H(2)O isomeric complexes, three CH(2)NOH···(H(2)O)(2) ones and one (CH(2)NOH)(2)···H(2)O complex. The analysis of the experimental spectra and their comparison with theoretical ones indicated that both the 1:1 and 1:2 complexes trapped in solid argon have the most stable cyclic structures stabilized by the O-H···O and O-H···N bonds between the formaldoxime and water molecules. In the 1:2 complex formaldoxime interacts with the water dimer, one H(2)O molecule acts as a proton acceptor for the OH group of formaldoxime whereas the second H(2)O molecule acts as a proton donor toward the nitrogen atom of the formaldoxime molecule. In the (CH(2)NOH)(2)···H(2)O complex the OH group of the water molecule acts as a proton donor toward one of the oxygen atoms of the formaldoxime cyclic dimer.
Collapse
Affiliation(s)
- Barbara Golec
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wrocław, Poland
| | | | | |
Collapse
|
35
|
RIAHI SIAVASH, EYNOLLAHI SOLMAZ, GANJALI MOHAMMADREZA. INTERACTION OF EMODIN WITH DNA BASES: A DENSITY FUNCTIONAL THEORY. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633610006055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In this study, we present work on the physicochemical interaction between the anticancer drug molecule Emodin (ED) and DNA. Comprehending the physicochemical properties of this drug besides the mechanism by which it interacts with DNA should eventually permit the rational design of novel anticancer or antiviral drugs. The final purpose is the clarification of this novel class of drugs as potential pharmaceutical agents. The properties of the isolated intercalator ED and its stacking interactions with adenine⋯thymine (AT) and guanine⋯cytosine (GC) (nucleic acid base pairs) in face-to-face and face-to-back models were studied by means of the density functional tightbinding (DFTB) method. This method was an approximate version of the density functional theory (DFT) method and it includes London dispersion energy. The molecular modeling of the complex formed between ED and DNA indicated that this complex was capable of contributing to the formation of a constant intercalation site. The results exhibit that ED changes affect DNA structure with reference to bond lengths, bond angles, torsion angles, and charges.
Collapse
Affiliation(s)
- SIAVASH RIAHI
- Institute of Petroleum Engineering, Faculty of Engineering, University of Tehran, P. O. Box 11365-4563, Tehran, Iran
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, Iran
| | - SOLMAZ EYNOLLAHI
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, Iran
| | - MOHAMMAD REZA GANJALI
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, P. O. Box 14155-6455, Tehran, Iran
| |
Collapse
|
36
|
D'Oria E, Novoa JJ. Cation-anion hydrogen bonds: a new class of hydrogen bonds that extends their strength beyond the covalent limit. A theoretical characterization. J Phys Chem A 2011; 115:13114-23. [PMID: 21942671 DOI: 10.1021/jp205176e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The existence of O-H···O hydrogen bonds having a strength within the -80 to -210 kcal/mol range, that is, in the range of strength of covalent bonds and well beyond the so-called covalent limit (-50 kcal/mol), is reported on complexes where the O-H proton donor and O acceptor groups are located in ions of opposite sign. A complete analysis of short distance O-H···O hydrogen bonds between charged fragments was performed for cases where the OH and O groups are both located on charged molecules. It shows that these interactions (a) are nonsymmetrical for the O-H and H···O distances, (b) have a noncovalent H···O bond critical point, and (c) have a strong and energetically stable electrostatic component when the OH and O groups are located in oppositely charged molecules. These cation-anion O-H···O interactions are energetically stable, satisfy the usual topology for hydrogen bonds, HBs, and also have the same directionality found in other HBs. Therefore, they should be considered as a new class of HBs, the cation-anion hydrogen bonds.
Collapse
Affiliation(s)
- Emiliana D'Oria
- Departament de Química Física, and IQTCUB, Facultat de Química, Universitat de Barcelona, Barcelona, Spain
| | | |
Collapse
|
37
|
Sheng XW, Mentel L, Gritsenko OV, Baerends EJ. Counterpoise correction is not useful for short and Van der Waals distances but may be useful at long range. J Comput Chem 2011; 32:2896-901. [PMID: 21735451 DOI: 10.1002/jcc.21872] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 05/05/2011] [Accepted: 05/25/2011] [Indexed: 11/12/2022]
Abstract
This article investigates the errors in supermolecule calculations for the helium dimer. In a full CI calculation, there are two errors. One is the basis set superposition error (BSSE), the other is the basis set convergence error (BSCE). Both of the errors arise from the incompleteness of the basis set. These two errors make opposite contributions to the interaction energies. The BSCE is by far the largest error in the short range and larger than (but much closer to) BSSE around the Van der Waals minimum. Only at the long range, the BSSE becomes the larger error. The BSCE and BSSE largely cancel each other over the Van der Waals well. Accordingly, it may be recommended to not include the BSSE for the calculation of the potential energy curve from short distance till well beyond the Van der Waals minimum, but it may be recommended to include the BSSE correction if an accurate tail behavior is required. Only if the calculation has used a very large basis set, one can refrain from including the counterpoise correction in the full potential range. These results are based on full CI calculations with the aug-cc-pVXZ (X = D, T, Q, 5) basis sets.
Collapse
Affiliation(s)
- Xiao Wei Sheng
- The Institute of Atomic and Molecular physics, Sichuan University, Chengdu, Sichuan 610065, China
| | | | | | | |
Collapse
|
38
|
Mata I, Molins E, Alkorta I, Espinosa E. Tuning the Interaction Energy of Hydrogen Bonds: The Effect of the Substituent. J Phys Chem A 2011; 115:12561-71. [DOI: 10.1021/jp202917z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ignasi Mata
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Bellaterra, Spain
| | - Elies Molins
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Bellaterra, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
| | - Enrique Espinosa
- Laboratorie de Cristallographie, Résonance Magnétique et Modélisations, CRM2, UMR CNRS 7036, Institut Jean Barriol, Nancy-Université, BP 70239, 54506 Vandoeuvre-lès-Nancy, France
| |
Collapse
|
39
|
Plumley JA, Dannenberg JJ. A comparison of the behavior of functional/basis set combinations for hydrogen-bonding in the water dimer with emphasis on basis set superposition error. J Comput Chem 2011; 32:1519-27. [PMID: 21328398 PMCID: PMC3073166 DOI: 10.1002/jcc.21729] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 11/07/2010] [Accepted: 11/09/2010] [Indexed: 11/07/2022]
Abstract
We evaluate the performance of ten functionals (B3LYP, M05, M05-2X, M06, M06-2X, B2PLYP, B2PLYPD, X3LYP, B97D, and MPWB1K) in combination with 16 basis sets ranging in complexity from 6-31G(d) to aug-cc-pV5Z for the calculation of the H-bonded water dimer with the goal of defining which combinations of functionals and basis sets provide a combination of economy and accuracy for H-bonded systems. We have compared the results to the best non-density functional theory (non-DFT) molecular orbital (MO) calculations and to experimental results. Several of the smaller basis sets lead to qualitatively incorrect geometries when optimized on a normal potential energy surface (PES). This problem disappears when the optimization is performed on a counterpoise (CP) corrected PES. The calculated interaction energies (ΔEs) with the largest basis sets vary from -4.42 (B97D) to -5.19 (B2PLYPD) kcal/mol for the different functionals. Small basis sets generally predict stronger interactions than the large ones. We found that, because of error compensation, the smaller basis sets gave the best results (in comparison to experimental and high-level non-DFT MO calculations) when combined with a functional that predicts a weak interaction with the largest basis set. As many applications are complex systems and require economical calculations, we suggest the following functional/basis set combinations in order of increasing complexity and cost: (1) D95(d,p) with B3LYP, B97D, M06, or MPWB1k; (2) 6-311G(d,p) with B3LYP; (3) D95++(d,p) with B3LYP, B97D, or MPWB1K; (4) 6-311++G(d,p) with B3LYP or B97D; and (5) aug-cc-pVDZ with M05-2X, M06-2X, or X3LYP.
Collapse
Affiliation(s)
- Joshua A. Plumley
- Department of Chemistry, Hunter College and the Graduate School, City University of New York, 695 Park Avenue, New York, New York 10065
| | - J. J. Dannenberg
- Department of Chemistry, Hunter College and the Graduate School, City University of New York, 695 Park Avenue, New York, New York 10065
| |
Collapse
|
40
|
Ji-Min J. M. Yan Y, Williams DE. Quantum-chemical investigation on hydrogen bonding interaction of hydrogen fluoride dimer at various mutual orientations. CHINESE J CHEM 2011. [DOI: 10.1002/cjoc.19900080103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
41
|
Alkorta I, Elguero J. Modeling the allosteric effect: modification of the tautomerism by intermolecular interactions and extension to molecular wires. Struct Chem 2011. [DOI: 10.1007/s11224-011-9749-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
42
|
Thanthiriwatte KS, Hohenstein EG, Burns LA, Sherrill CD. Assessment of the Performance of DFT and DFT-D Methods for Describing Distance Dependence of Hydrogen-Bonded Interactions. J Chem Theory Comput 2010; 7:88-96. [PMID: 26606221 DOI: 10.1021/ct100469b] [Citation(s) in RCA: 323] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Noncovalent interactions such as hydrogen bonds, van der Waals forces, and π-π interactions play important roles influencing the structure, stability, and dynamic properties of biomolecules including DNA and RNA base pairs. In an effort to better understand the fundamental physics of hydrogen bonding (H-bonding), we investigate the distance dependence of interaction energies in the prototype bimolecular complexes of formic acid, formamide, and formamidine. Potential energy curves along the H-bonding dissociation coordinate are examined both by establishing reference CCSD(T) interaction energies extrapolated to the complete basis set limit and by assessing the performance of the density functional methods B3LYP, PBE, PBE0, B970, PB86, M05-2X, and M06-2X and empirical dispersion corrected methods B3LYP-D3, PBE-D3, PBE0-D3, B970-D2, BP86-D3, and ωB97X-D, with basis sets 6-311++G(3df,3pd), aug-cc-pVDZ, and aug-cc-pVTZ. Although H-bonding interactions are dominated by electrostatics, it is necessary to properly account for dispersion interactions to obtain accurate energetics. In order to quantitatively probe the nature of hydrogen bonding interactions as a function of distance, we decompose the interaction energy curves into physically meaningful components with symmetry-adapted perturbation theory (SAPT). The SAPT results confirm that the contribution of dispersion and induction are significant at and near equilibrium, although electrostatics dominate. Among the DFT/DFT-D techniques, the best overall results are obtained utilizing counterpoise-corrected ωB97X-D with the aug-cc-pVDZ basis set.
Collapse
Affiliation(s)
- Kanchana S Thanthiriwatte
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Edward G Hohenstein
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Lori A Burns
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| |
Collapse
|
43
|
Alkorta I, Elguero J, Popelier PL. Thermodynamic and kinetic effects of Lewis acid complexation on a Schiff base present in two tautomeric forms. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1813] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
44
|
Baranyai A, Kiss PT. A transferable classical potential for the water molecule. J Chem Phys 2010; 133:144109. [DOI: 10.1063/1.3490660] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
|
45
|
Ganjali MR, Larijani B, Shams H, Riahi S, Faridbod F, Norouzi P. Using dextromethorphan potentiometric membrane sensor in analysis of dextromethorphan hydrobromide in pharmaceutical formulation and urine; Computational study. JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.1134/s1061934810100114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
46
|
Riahi S, Eynollahi S, Ganjali MR. Computational Studies on Effects of MDMA as an Anticancer Drug on DNA. Chem Biol Drug Des 2010; 76:425-32. [DOI: 10.1111/j.1747-0285.2010.01027.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
47
|
Wang WZ, Pu XM, Zheng WX, Wong NB, Tian AM. On the Importance of CP-corrected Gradient Optimization in the Study of Hydrogen Bonded Systems. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.20030211214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
48
|
Song D, Su H, Kong FA, Lin SH. Anharmonic RRKM Calculation for the Dissociation of (H2O)2H+ and Its Deuterated Species (D2O)2D+. J Phys Chem A 2010; 114:10217-24. [DOI: 10.1021/jp103782r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Di Song
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China, Institute of Applied Chemistry, Institute of Molecular Science, Chiao-Tung University, Hsin-Chu, Taiwan, Republic of China, and Institute of Atomic and Molecular Science, Academia Sinica, P.O. Box 23-166, Taipei, Taiwan, Republic of China,
| | - Hongmei Su
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China, Institute of Applied Chemistry, Institute of Molecular Science, Chiao-Tung University, Hsin-Chu, Taiwan, Republic of China, and Institute of Atomic and Molecular Science, Academia Sinica, P.O. Box 23-166, Taipei, Taiwan, Republic of China,
| | - Fan-ao Kong
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China, Institute of Applied Chemistry, Institute of Molecular Science, Chiao-Tung University, Hsin-Chu, Taiwan, Republic of China, and Institute of Atomic and Molecular Science, Academia Sinica, P.O. Box 23-166, Taipei, Taiwan, Republic of China,
| | - Sheng-Hsien Lin
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China, Institute of Applied Chemistry, Institute of Molecular Science, Chiao-Tung University, Hsin-Chu, Taiwan, Republic of China, and Institute of Atomic and Molecular Science, Academia Sinica, P.O. Box 23-166, Taipei, Taiwan, Republic of China,
| |
Collapse
|
49
|
Luo D, Zhang N, Hong S, Wu H, Liu Z. Complexes in the photocatalytic reaction of CO(2) and H(2)O: theoretical studies. Int J Mol Sci 2010; 11:2792-804. [PMID: 21152274 PMCID: PMC2996739 DOI: 10.3390/ijms11082792] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Revised: 07/16/2010] [Accepted: 07/18/2010] [Indexed: 11/16/2022] Open
Abstract
Complexes (H2O/CO2, e–(H2O/CO2) and h+–(H2O/CO2)) in the reaction system of CO2 photoreduction with H2O were researched by B3LYP and MP2 methods along with natural bond orbital (NBO) analysis. Geometries of these complexes were optimized and frequencies analysis performed. H2O/CO2 captured photo-induced electron and hole produced e–(H2O/CO2) and h+–(H2O/CO2), respectively. The results revealed that CO2 and H2O molecules could be activated by the photo-induced electrons and holes, and each of these complexes possessed two isomers. Due to the effect of photo-induced electrons, the bond length of C=O and H-O were lengthened, while H-O bonds were shortened, influenced by holes. The infrared (IR) adsorption frequencies of these complexes were different from that of CO2 and H2O, which might be attributed to the synergistic effect and which could not be captured experimentally.
Collapse
Affiliation(s)
- Dongmei Luo
- Department of Chemistry, Nanchang University, Nanchang 330031, China; E-Mails: (D.L.); (S.H.); (H.W.); (Z.L.)
- Department of Chemistry, QiqihaerUniversity, Qiqihaer 161006, China
| | - Ning Zhang
- Department of Chemistry, Nanchang University, Nanchang 330031, China; E-Mails: (D.L.); (S.H.); (H.W.); (Z.L.)
- *Author to whom correspondence should be addressed; E-Mail: ; Tel.: +86-791-3969-332; Fax: +86-791-3969-338
| | - Sanguo Hong
- Department of Chemistry, Nanchang University, Nanchang 330031, China; E-Mails: (D.L.); (S.H.); (H.W.); (Z.L.)
| | - Huanwen Wu
- Department of Chemistry, Nanchang University, Nanchang 330031, China; E-Mails: (D.L.); (S.H.); (H.W.); (Z.L.)
| | - Zhihua Liu
- Department of Chemistry, Nanchang University, Nanchang 330031, China; E-Mails: (D.L.); (S.H.); (H.W.); (Z.L.)
| |
Collapse
|
50
|
Abstract
Spectroscopic characterizations of the stereochemistry of complexes of ammonia (NH(3)) have strongly confirmed some long-held ideas about the weak interactions of NH(3) while casting doubt on others. As expected, NH(3) is observed to be a nearly universal proton acceptor, accepting hydrogen bonds from even some of the weakest proton donors. Surprisingly, no evidence has been found to support the view that NH(3) acts as a proton donor through hydrogen bonding. A critical evaluation of the work that has been done to gather such evidence, as well as of earlier work involving condensed-phase observations, suggests that NH(3) might well be best described as a powerful hydrogen-bond acceptor with little propensity to donate hydrogen bonds.
Collapse
|