1
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Milovanović B, Stanojević A, Etinski M, Petković M. Intriguing Intermolecular Interplay in Guanine Quartet Complexes with Alkali and Alkaline Earth Cations. J Phys Chem B 2020; 124:3002-3014. [DOI: 10.1021/acs.jpcb.0c01165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Branislav Milovanović
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade, Serbia
| | - Ana Stanojević
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade, Serbia
| | - Mihajlo Etinski
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade, Serbia
| | - Milena Petković
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12-16, 11158 Belgrade, Serbia
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2
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Zhang P, Ji X, Zhang H, Xia B. Quantum investigation into intermolecular interactions between bisphenol A and 2-vinyl/4-vinylpyridine: Theoretical insight into molecular imprinting complexes. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.03.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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3
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Salehzadeh S, Maleki F. New equation for calculating total interaction energy in one noncyclic ABC triad and new insights into cooperativity of noncovalent bonds. J Comput Chem 2016; 37:2799-2807. [PMID: 27753119 DOI: 10.1002/jcc.24505] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/02/2016] [Accepted: 09/07/2016] [Indexed: 11/10/2022]
Abstract
In this work, a new equation consist of A⋅⋅⋅B, B⋅⋅⋅C, A⋅⋅⋅BC, and AB⋅⋅⋅C interactions is proposed for calculating the total interaction energy of noncyclic ABC triads. New equations are also proposed for calculating the changes in values of A⋅⋅⋅B and B⋅⋅⋅C interactions on the formation of triad from the corresponding dyads. The advantages of equations proposed here in comparison with many-body interaction energy approach are discussed. All proposed equations were tested in F3 MLi⋅⋅⋅NCH⋅⋅⋅HLH and F3 MLi⋅⋅⋅HLH⋅⋅⋅HCN (M = C, Si; L = Be, Mg) as well as H3 N⋅⋅⋅XY⋅⋅⋅HF (X, Y = F, Cl, Br) noncyclic A⋅⋅⋅B⋅⋅⋅C triads. The data show that the total cooperativity of triad correlates well with the sum of the changes in values of A⋅⋅⋅B and B⋅⋅⋅C interactions calculated through new equations proposed here. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Farahnaz Maleki
- Department of Chemistry, Bu-Ali Sina University, Hamedan, Iran
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4
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Ghiasi R, Heidarbeigi A. Substituent effect on the structure and properties of dialumene. RUSS J INORG CHEM+ 2016. [DOI: 10.1134/s0036023616080088] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Probing the nature of the Co(III) ion in cobalamins: The ligand substitution reactions of aquacyanocobester, aquacyano(10-nitro)cobester and aquacyano(10-amino)cobester. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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6
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Computational investigation on the intramolecular resonance-inhibited hydrogen bonding: a new type of interaction versus the RAHB model. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1683-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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7
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Łukomska M, Rybarczyk-Pirek AJ, Jabłoński M, Palusiak M. The nature of NO-bonding in N-oxide group. Phys Chem Chem Phys 2015; 17:16375-87. [PMID: 26051488 DOI: 10.1039/c5cp02148k] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The nature of the NO-bond in the N-oxide group was investigated by means of combined theoretical calculations (including QTAIM and NBO approaches) and statistical analyses of the contents of crystal structure databases. The N-O bond in the N-oxide group should be classified as the NO donating bond with an important contribution of ON back-donation (of the π-electron type, when available). The visualization of the Laplacian of electron density in the region of an oxygen valence sphere suggests the presence of two lone pairs for the imine-N-oxide group (characterized by effective ON back-donation). A detailed bonding analysis performed by means of natural resonance theory indicates that the N→O bond is of an order of magnitude clearly greater than 1. In addition, the stability of the N→O bond in various N-oxides was estimated. The analyses of the hydrogen- and halogen-bonded complexes of the N-oxides reveal strong Lewis basicity of the N-oxide group. The formation of H- and X-bonding leads to N→O bond elongation due to its structural, topological and spectroscopic characteristics. Moreover, in pyridine-N-oxide, the electron-withdrawing -NO2 group additionally stabilizes the N→O bond, whereas the opposite effect can be observed for the electron-donating-NH2 substituent. This is due to a substituent effect on the π-type ON back-donation. As a result, the oxygen atom in pyridine-N-oxide may change its availability during intermolecular interaction formation, as revealed in the interaction energy, which changes by about half of the estimated total interaction energy.
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Affiliation(s)
- Marlena Łukomska
- Department of Theoretical and Structural Chemistry, Faculty of Chemistry, University of Łódź, 163/165 Pomorska St., 90-236 Łódź, Poland.
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8
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Villanueva EF, Mó O, Yáñez M. On the existence and characteristics of π-beryllium bonds. Phys Chem Chem Phys 2015; 16:17531-6. [PMID: 25026560 DOI: 10.1039/c4cp01992j] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The existence of π-beryllium bonds explains the stability of the complexes between ethylene and acetylene and BeX2 (X = H, F, and Cl) derivatives. These linkers involve a significant charge transfer from the π(CC) bonding orbitals into the empty p orbitals of Be and to a much smaller degree into the σ(BeH)* antibonding orbitals. The significant deformation of the BeX2 moiety and the slight deformation of the unsaturated hydrocarbon result in distortion energies as high as the dissociation energy of the complex. The π-beryllium bonds are about four times stronger than conventional π-hydrogen bonds and even stronger than the strongest π-hydrogen bond reported to date in the literature. The topology of their electron density is characterized as being very flat in the bonding region between the π-system and Be, which leads to topologically unstable structures close to catastrophe points. Among the functionals considered in our study M06 is the one that leads to values in better agreement with CCSD(T)/aug-cc-pVTZ calculations used as a reference. B3LYP underestimates some interactions, whereas M06-2X overestimates all of them. MP2 also yields good agreement with the CCSD(T) method.
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Affiliation(s)
- Estefanía Fernández Villanueva
- Departamento de Química, Facultad de Ciencias, Módulo 13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain.
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9
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Albrecht L, Boyd RJ. Atomic energy analysis of cooperativity, anti-cooperativity, and non-cooperativity in small clusters of methanol, water, and formaldehyde. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.08.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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10
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Kabanda MM, Tran VT, Tran QT, Ebenso EE. A computational study of pyrazinamide: Tautomerism, acid–base properties, micro-solvation effects and acid hydrolysis mechanism. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.07.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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11
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Liu H, Man R, Wang Z, Liao J, Li X, Ma S, Yi P. Study on the cooperativity of hydrogen bonds between H2Y and HX (X = F, Cl, Br; Y = O, S, Se). JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1142/s0219633614500370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The structure characteristics, interaction energies, cooperative energies of the complexes between chalcogen hydrides ( H 2 Y ) and halogen hydrides (HX) have been studied theoretically at the MP2 level with aug-cc-pVTZ basis set in this paper. The conclusions show that there are strong interactions between H 2 Y and HX. The stability of the complex is decided by the electronegativity of the negatively charged atom. The cooperativity is observed in the two or three hydrogen bonds of each trimer structures in title system. The values of the cooperative energies and the cooperative contributions all illustrate that the cooperativity is of great importance in these complexes. The "atoms in molecules" (AIM) analyses show that the complexes in title system are mainly electrostatic interactions (closed-shell interactions) in character. For H ⋯ O bonds in H 2 O ⋯ HF ⋯ H 2 O , H 2 O ⋯ HBr ⋯ H 2 O and HF ⋯ H 2 O ⋯ HF , the 1 < |Vc|/Gc < 2 and -Gc < Hc < 0 indicate the interactions in these compounds are between closed-shell interaction and opened-shell interaction.
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Affiliation(s)
- Hexiu Liu
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
- School of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Ruilin Man
- School of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Zhaoxu Wang
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
| | - Jianping Liao
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
| | - Xiaofang Li
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
| | - Songjiang Ma
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
| | - Pinggui Yi
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
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12
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Albrecht L, Boyd RJ, Mó O, Yáñez M. Changing Weak Halogen Bonds into Strong Ones through Cooperativity with Beryllium Bonds. J Phys Chem A 2014; 118:4205-13. [DOI: 10.1021/jp503229u] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Laura Albrecht
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Russell J. Boyd
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Otilia Mó
- Departamento
de Quı́mica, Facultad de Ciencias, Módulo
13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Manuel Yáñez
- Departamento
de Quı́mica, Facultad de Ciencias, Módulo
13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
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13
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Abstract
Positive cooperativity is found in beryllium bonded complexes similar to that described for hydrogen bonded systems.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica (IQM-CSIC)
- 28006-Madrid, Spain
| | - José Elguero
- Instituto de Química Médica (IQM-CSIC)
- 28006-Madrid, Spain
| | - Manuel Yáñez
- Departamento de Química
- Módulo 13
- Universidad Autónoma de Madrid
- Campus de Excelencia UAM-CSIC
- 28049 Madrid, Spain
| | - Otilia Mó
- Departamento de Química
- Módulo 13
- Universidad Autónoma de Madrid
- Campus de Excelencia UAM-CSIC
- 28049 Madrid, Spain
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14
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Gillan MJ, Alfè D, Bartók AP, Csányi G. First-principles energetics of water clusters and ice: A many-body analysis. J Chem Phys 2013; 139:244504. [DOI: 10.1063/1.4852182] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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KABANDA MWADHAMM, EBENSO ENOE. DFT STUDY OF THE PROTONATION AND DEPROTONATION ENTHALPIES OF BENZOXAZOLE, 1,2-BENZISOXAZOLE AND 2,1-BENZISOXAZOLE AND IMPLICATIONS FOR THE STRUCTURES AND ENERGIES OF THEIR ADDUCTS WITH EXPLICIT WATER MOLECULES. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613500703] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Benzoxazole, 1,2-benzisoxazole and 2,1-benzisoxazole are biologically active molecules with potential applications in drug design. Their interaction with aqueous medium in biological systems may be simulated by considering their interaction with explicit water molecules. Such studies provide information on the structures, energies and type of interactions stabilizing the resulting geometric systems. The objective of the current study was to utilize theoretical approaches to investigate the structures, stabilization energy and binding energy of benzoxazole–water, 1,2-benzisoxazole–water and 2,1-benzisoxazole–water complexes. The calculations were performed utilizing the density functional theory (DFT)/M06-2X/6-311 ++ G(d,p) method and the DFT/ωB97XD method with both the 6-311 ++ G(d,p) and the aug-cc-pVDZ basis sets. The results suggest that the stability of the different clusters depends on interrelated factors including the rings formed by intermolecular hydrogen bonds and the proton affinity (PA) or acidity of the atoms forming the intermolecular hydrogen bonds with the water molecules. A comparison across methods indicates that the results follow similar trends with different methods.
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Affiliation(s)
- MWADHAM M. KABANDA
- Material Science Innovation and Modelling (MaSIM) Research Focus Area, Faculty of Agriculture, Science and Technology, North-West University (Mafikeng Campus), Private Bag X2046, Mmabatho 2735, South Africa
| | - ENO E. EBENSO
- Material Science Innovation and Modelling (MaSIM) Research Focus Area, Faculty of Agriculture, Science and Technology, North-West University (Mafikeng Campus), Private Bag X2046, Mmabatho 2735, South Africa
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16
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Molecular insight into the amine–water interaction: A combined vibrational, energetic and NBO/NEDA study. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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17
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Ghiasi R, Manochehri M, Yadegari N. A quantum chemistry study of ruthenabenzene complexes. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2013. [DOI: 10.1134/s0036024413090331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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18
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Malenov DP, Janjić GV, Veljković DŽ, Zarić SD. Mutual influence of parallel, CH/O, OH/π and lone pair/π interactions in water/benzene/water system. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.05.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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19
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Mathura S, Sannasy D, de Sousa AS, Perry CB, Navizet I, Marques HM. The preparation of N-acetyl-Co(III)-microperoxidase-8 (NAcCoMP8) and its ligand substitution reactions: A comparison with aquacobalamin (vitamin B12a). J Inorg Biochem 2013; 123:66-79. [DOI: 10.1016/j.jinorgbio.2013.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 03/01/2013] [Accepted: 03/04/2013] [Indexed: 12/01/2022]
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20
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Qi HW, Leverentz HR, Truhlar DG. Water 16-mers and hexamers: assessment of the three-body and electrostatically embedded many-body approximations of the correlation energy or the nonlocal energy as ways to include cooperative effects. J Phys Chem A 2013; 117:4486-99. [PMID: 23627665 DOI: 10.1021/jp401463f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
This work presents a new fragment method, the electrostatically embedded many-body expansion of the nonlocal energy (EE-MB-NE), and shows that it, along with the previously proposed electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE), produces accurate results for large systems at the level of CCSD(T) coupled cluster theory. We primarily study water 16-mers, but we also test the EE-MB-CE method on water hexamers. We analyze the distributions of two-body and three-body terms to show why the many-body expansion of the electrostatically embedded correlation energy converges faster than the many-body expansion of the entire electrostatically embedded interaction potential. The average magnitude of the dimer contributions to the pairwise additive (PA) term of the correlation energy (which neglects cooperative effects) is only one-half of that of the average dimer contribution to the PA term of the expansion of the total energy; this explains why the mean unsigned error (MUE) of the EE-PA-CE approximation is only one-half of that of the EE-PA approximation. Similarly, the average magnitude of the trimer contributions to the three-body (3B) term of the EE-3B-CE approximation is only one-fourth of that of the EE-3B approximation, and the MUE of the EE-3B-CE approximation is one-fourth that of the EE-3B approximation. Finally, we test the efficacy of two- and three-body density functional corrections. One such density functional correction method, the new EE-PA-NE method, with the OLYP or the OHLYP density functional (where the OHLYP functional is the OptX exchange functional combined with the LYP correlation functional multiplied by 0.5), has the best performance-to-price ratio of any method whose computational cost scales as the third power of the number of monomers and is competitive in accuracy in the tests presented here with even the electrostatically embedded three-body approximation.
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Affiliation(s)
- Helena W Qi
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, USA
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21
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Ch'ng LC, Samanta AK, Wang Y, Bowman JM, Reisler H. Experimental and theoretical investigations of the dissociation energy (D0) and dynamics of the water trimer, (H2O)3. J Phys Chem A 2013; 117:7207-16. [PMID: 23536966 DOI: 10.1021/jp401155v] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a joint experimental-theoretical study of the predissociation dynamics of the water trimer following excitation of the hydrogen bonded OH-stretch fundamental. The bond dissociation energy (D0) for the (H2O)3 → H2O + (H2O)2 dissociation channel is determined from fitting the speed distributions of selected rovibrational states of the water monomer fragment using velocity map imaging. The experimental value, D0 = 2650 ± 150 cm(-1), is in good agreement with the previously determined theoretical value, 2726 ± 30 cm(-1), obtained using an ab initio full-dimensional potential energy surface (PES) together with Diffusion Monte Carlo calculations [ Wang ; Bowman . J. Chem. Phys. 2011 , 135 , 131101 ]. Comparing this value to D0 of the dimer places the contribution of nonpairwise additivity to the hydrogen bonding at 450-500 cm(-1). Quasiclassical trajectory (QCT) calculations using this PES help elucidate the reaction mechanism. The trajectories show that most often one hydrogen bond breaks first, followed by breaking and re-forming of hydrogen bonds (often with different hydrogen bonds breaking) until, after many picoseconds, a water monomer is finally released. The translational energy distributions calculated by QCT for selected rotational levels of the monomer fragment agree with the experimental observations. The product translational and rotational energy distributions calculated by QCT also agree with statistical predictions. The availability of low-lying intermolecular vibrational levels in the dimer fragment is likely to facilitate energy transfer before dissociation occurs, leading to statistical-like product state distributions.
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Affiliation(s)
- Lee C Ch'ng
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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22
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DFT Studies of Trans and Cis Influences in the Homolysis of the Co–C Bond in Models of the Alkylcobalamins. J Phys Chem A 2013; 117:3057-68. [DOI: 10.1021/jp311788t] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Zhou Y, ul Hassan S, Zhang L, Li X, Ahmad W. Supramolecular Self-Assembly of V-Shaped Water Trimers and Diethylenetriamine Molecules in a New Solid State Ferrous Molybdenum(V) Phosphate. J CLUST SCI 2013. [DOI: 10.1007/s10876-012-0545-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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24
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Kabanda MM, Ebenso EE. Structures, Stabilization Energies, and Binding Energies of Quinoxaline···(H2O)n, Quinoxaline Dimer, and Quinoxaline···Cu Complexes: A Theoretical Study. J Phys Chem A 2013; 117:1583-95. [PMID: 23343309 DOI: 10.1021/jp309356b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mwadham M. Kabanda
- Department of Chemistry, North-West University (Mafikeng Campus), Private Bag x2046, Mmabatho 2735,
South Africa
| | - Eno E. Ebenso
- Department of Chemistry, North-West University (Mafikeng Campus), Private Bag x2046, Mmabatho 2735,
South Africa
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25
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Vallejos MM, Lamsabhi AM, Peruchena NM, Mó O, Yáñez M. Microsolvation of morpholine, a bidentate base - the importance of cooperativity. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Margarita M. Vallejos
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura; Universidad Nacional del Nordeste; Avda. Libertad 5460 (3400) Corrientes Argentina
| | - Al Mokhtar Lamsabhi
- Departamento de Química, Facultad de Ciencias, Módulo 13, Campus de Excelencia UAM-CSIC; Universidad Autónoma de Madrid; Cantoblanco 28049 Madrid Spain
| | - Nélida M. Peruchena
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura; Universidad Nacional del Nordeste; Avda. Libertad 5460 (3400) Corrientes Argentina
| | - Otilia Mó
- Departamento de Química, Facultad de Ciencias, Módulo 13, Campus de Excelencia UAM-CSIC; Universidad Autónoma de Madrid; Cantoblanco 28049 Madrid Spain
| | - Manuel Yáñez
- Departamento de Química, Facultad de Ciencias, Módulo 13, Campus de Excelencia UAM-CSIC; Universidad Autónoma de Madrid; Cantoblanco 28049 Madrid Spain
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26
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Brea O, Yáñez M, Mó O, Lamsabhi AM. On the stability of [(uracil)2-Cu]2+ complexes in the gas phase. Different pathways for the formation of [(uracil-H)(uracil)-Cu]+ monocations. Org Biomol Chem 2013; 11:3862-70. [DOI: 10.1039/c3ob40450a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Govender PP, Navizet I, Perry CB, Marques HM. The cis influence of the corrin in vitamin B12 models. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.08.061] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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28
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Albrecht L, Boyd RJ, Mó O, Yáñez M. Cooperativity between hydrogen bonds and beryllium bonds in (H2O)(n)BeX2 (n = 1-3, X = H, F) complexes. A new perspective. Phys Chem Chem Phys 2012; 14:14540-7. [PMID: 23014263 DOI: 10.1039/c2cp42534c] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction of BeX(2) (X = H, F) with water molecules has been analyzed at the B3LYP/6-311+G(3df,2p)//B3LYP/6-311+G(d,p) level of theory. The formation of strong beryllium bonds between water molecules and the BeX(2) derivative triggers significant electron density redistribution within the whole system, resulting in significant changes in the proton donor and proton acceptor capacity of the water molecules involved. Hence, significant cooperative and anti-cooperative effects are present, explaining why there is no case in which the global minimum corresponds to a tetracoordinated beryllium atom. In fact, the most stable clusters can be viewed as the result of the attachment of BeX(2) to the water trimer and the water dimer, respectively, and not as the result of the solvation of the BeX(2) molecule. We have also shown that the decomposition of the interaction energy into atomic components is a reliable quantitative tool to describe all the closed-shell interactions present in the clusters investigated herein, namely hydrogen bonds, beryllium bonds and dihydrogen bonds. Indeed, we have shown that the changes in the atomic energy components are correlated with the changes in the strength of these interactions, and they provide a quantitative measure of cooperative effects directly in terms of energies.
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Affiliation(s)
- Laura Albrecht
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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Navizet I, Perry CB, Govender PP, Marques HM. cis Influence in Models of Cobalt Corrins by DFT and TD-DFT Studies. J Phys Chem B 2012; 116:8836-45. [DOI: 10.1021/jp304007a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Isabelle Navizet
- Molecular Sciences
Institute, School of Chemistry, University of Witwatersrand, P.O. Wits, Johannesburg, 2050 South
Africa
| | - Christopher B. Perry
- Molecular Sciences
Institute, School of Chemistry, University of Witwatersrand, P.O. Wits, Johannesburg, 2050 South
Africa
| | - Penny P. Govender
- Molecular Sciences
Institute, School of Chemistry, University of Witwatersrand, P.O. Wits, Johannesburg, 2050 South
Africa
- Department
of Applied
Chemistry, University of Johannesburg, P.O. Box 17011, Doornfontein, Johannesburg, 2028 South Africa
| | - Helder M. Marques
- Molecular Sciences
Institute, School of Chemistry, University of Witwatersrand, P.O. Wits, Johannesburg, 2050 South
Africa
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Mó O, Yáñez M, Alkorta I, Elguero J. Modulating the Strength of Hydrogen Bonds through Beryllium Bonds. J Chem Theory Comput 2012; 8:2293-300. [PMID: 26588962 DOI: 10.1021/ct300243b] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mutual influence between beryllium bonds and inter- or intramolecular hydrogen bonds (HBs) has been investigated at the B3LYP/6-311++G(3df,2p) level of theory, using the complexes between imidazole dimer and malonaldehyde with BeH2 and BeF2 as suitable model systems. Imidazole and its dimer form very strong beryllium bonds with both BeH2 and BeF2, accompanied by a significant geometry distortion of the Lewis acid. More importantly, we have found a clear cooperativity between these two noncovalent interactions, since the intermolecular HB between the two imidazole molecules in the dimer-BeX2 complex becomes much stronger than in the isolated dimer, whereas the beryllium bond becomes also stronger in the dimer-BeX2 complex, with respect to that found in the imidazole-BeX2 complex. The effects of beryllium bonds are also dramatic on the strength of intramolecular HBs. Depending on to which center the BeX2 is attached, the intramolecular HB becomes much stronger or much weaker. The first situation is found when the beryllium derivative is attached to the HB donor, whereas the second occurs if it is attached to the HB acceptor. The first effect can be so strong as to produce a spontaneous proton transfer, as it is actually the case of the malonaldehyde-BeF2 complex.
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Affiliation(s)
- Otilia Mó
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid , Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Manuel Yáñez
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid , Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC) , Juan de la Cierva, 3, 28006-Madrid, Spain
| | - José Elguero
- Instituto de Química Médica (CSIC) , Juan de la Cierva, 3, 28006-Madrid, Spain
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Vallejos MM, Peruchena NM. Preferential Formation of the Different Hydrogen Bonds and Their Effects in Tetrahydrofuran and Tetrahydropyran Microhydrated Complexes. J Phys Chem A 2012; 116:4199-210. [DOI: 10.1021/jp301498n] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Margarita M. Vallejos
- Laboratorio de Estructura
Molecular y Propiedades,
Área de Química Física, Departamento de Química,
Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avda. Libertad 5460,
(3400) Corrientes, Argentina
| | - Nélida M. Peruchena
- Laboratorio de Estructura
Molecular y Propiedades,
Área de Química Física, Departamento de Química,
Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avda. Libertad 5460,
(3400) Corrientes, Argentina
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Musso F, Mignon P, Ugliengo P, Sodupe M. Cooperative effects at water–crystalline silica interfaces strengthen surface silanol hydrogen bonding. An ab initio molecular dynamics study. Phys Chem Chem Phys 2012; 14:10507-14. [DOI: 10.1039/c2cp40756f] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bankiewicz B, Matczak P, Palusiak M. Electron Density Characteristics in Bond Critical Point (QTAIM) versus Interaction Energy Components (SAPT): The Case of Charge-Assisted Hydrogen Bonding. J Phys Chem A 2011; 116:452-9. [DOI: 10.1021/jp210940b] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Barbara Bankiewicz
- Department of Theoretical Chemistry, University of Białystok, Hurtowa 1, 15-399, Białystok, Poland
| | - Piotr Matczak
- Department of Theoretical and Structural Chemistry, University of Łódź, Tamka 12, 91-403 Łódź, Poland
| | - Marcin Palusiak
- Department of Theoretical and Structural Chemistry, University of Łódź, Tamka 12, 91-403 Łódź, Poland
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Paul BK, Guchhait N. A computational investigation on the intramolecular hydrogen bonding interaction and excited state intramolecular proton transfer process in 2-quinolin-2-yl-phenol. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.09.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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37
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Bankiewicz B, Palusiak M. Does electron density in bond critical point reflect the formal charge distribution in H-bridges? The case of charge-assisted hydrogen bonds (CAHBs). COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.02.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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38
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Ośmiałowski B, Krygowski TM, Dominikowska J, Palusiak M. The effect of benzoannulation on the transition state and the proton transfer equilibrium in di(2-pyridyl)methane derivatives. NEW J CHEM 2011. [DOI: 10.1039/c1nj20108e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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39
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The influence of secondary interactions on complex stability and double proton transfer reaction in 2-[1H]-pyridone/2-hydroxypyridine dimers. J Mol Model 2010; 17:2491-500. [PMID: 21193938 DOI: 10.1007/s00894-010-0934-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Accepted: 12/09/2010] [Indexed: 10/18/2022]
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Szatyłowicz H, Krygowski TM, Palusiak M, Poater J, Solà M. Routes of π-Electron Delocalization in 4-Substituted-1,2-benzoquinones. J Org Chem 2010; 76:550-6. [DOI: 10.1021/jo102065e] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Halina Szatyłowicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | | | - Marcin Palusiak
- Department of Chemistry, University of Łódź, Tamka 12, 91-403 Łódź, Poland
| | - Jordi Poater
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071 Girona, Catalonia, Spain
| | - Miquel Solà
- Institut de Química Computacional and Departament de Química, Universitat de Girona, Campus de Montilivi, 17071 Girona, Catalonia, Spain
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The physical chemistry of [M(H2O)4(NO3)2] (M = Mn2+, Co2+, Ni2+, Cu2+, Zn2+) complexes: computational studies of their structure, energetics and the topological properties of the electron density. Theor Chem Acc 2010. [DOI: 10.1007/s00214-010-0781-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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42
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Xu Y, Nadykto AB, Yu F, Jiang L, Wang W. Formation and properties of hydrogen-bonded complexes of common organic oxalic acid with atmospheric nucleation precursors. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.04.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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43
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Competition and cooperativity between hydrogen bond and σ-hole bond in SCS–(HF)n (n=1 and 2) systems. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.04.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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44
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Varfolomeev MA, Zaitseva KV, Rakipov IT, Solomonov BN. Enthalpy of cooperative hydrogen bonding in the complexes of triethyl- and tri-n-butylamines with alcohols: Effect of the alkyl chain length. RUSS J GEN CHEM+ 2010. [DOI: 10.1134/s1070363210030059] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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45
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McDowell SAC, Buckingham AD. Cooperative and diminutive hydrogen bonding in Y⋯HCN⋯HCN and NCH⋯Y⋯HCN trimers (Y=BF,CO,N2). J Chem Phys 2010; 132:064303. [PMID: 20151739 DOI: 10.1063/1.3297894] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Sean A C McDowell
- Department of Biological and Chemical Sciences, The University of the West Indies, Cave Hill Campus, P.O. Box 64, Bridgetown, Barbados.
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Chen HY, Hsu SCN, Kao CL. Microhydration of 9-methylguanine:1-methylcytosinebase pair and its radical anion: a density functional theory study. Phys Chem Chem Phys 2010; 12:1253-63. [DOI: 10.1039/b920603e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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47
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Varadwaj PR, Marques HM. The physical chemistry of coordinated aqua-, ammine-, and mixed-ligand Co2+ complexes: DFT studies on the structure, energetics, and topological properties of the electron density. Phys Chem Chem Phys 2010; 12:2126-38. [DOI: 10.1039/b919953e] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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48
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Toledo EJ, Custodio R, Ramalho TC, Porto MEG, Magriotis ZM. Electrical field effects on dipole moment, structure and energetic of (H2O)n (2⩽n⩽15) cluster. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.08.035] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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49
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Lenz A, Ojamäe L. A theoretical study of water equilibria: The cluster distribution versus temperature and pressure for (H2O)n, n=1–60, and ice. J Chem Phys 2009; 131:134302. [DOI: 10.1063/1.3239474] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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50
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Leyva V, Corral I, Gonzalez L. Ortho-Nitrobenzaldehyde 1:1 Water Complexes. The Influence of Solute Water Interactions in the Vertical Excited Spectrum. Z PHYS CHEM 2009. [DOI: 10.1524/zpch.2008.5387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Abstract
The intermolecular hydrogen bonding interaction of a water molecule with the caging group ortho-nitrobenzaldehyde (o-NBA) has been studied by means of quantum mechanical methods. The o-NBA chromophore presents two functional groups, NO2 and CHO, interconnected by an intramolecular hydrogen bond. Both groups compete for the interaction with the solvent molecule, leading to eleven possible stable isomers that are very close in energy. The effect of the binding water on the electronic properties of o-NBA has been analyzed in structural terms as well as using the atoms-in-molecules theory of Bader. Binding energies for all complexes are reported, and in general they range from 5 to 13 kJ/mol. Special attention has been paid to the effect of the water molecule on the vertical excitation energies of o-NBA. Upon water complexation the absorption spectrum of o-NBA shifts to higher energies and it is characterized by three bands of comparable intensities as those recently measured for o-NBA in gas phase.
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