1
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Calculations of R eẤ nyi entropy, Tsallis entropy and Onicescu information energy for helium, lithium and beryllium atoms using an analytic correlated wave function. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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2
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An X, Zhang W, Rong C, Liu S. Understanding
Ramachandran
plot for dipeptide: A density functional theory and i
nformation‐theoretic
approach study. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Xiaoyan An
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, (Ministry of Education of China) Hunan Normal University Changsha Hunan People's Republic of China
| | - Wenbiao Zhang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, (Ministry of Education of China) Hunan Normal University Changsha Hunan People's Republic of China
| | - Chunying Rong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, (Ministry of Education of China) Hunan Normal University Changsha Hunan People's Republic of China
| | - Shubin Liu
- Research Computing Center University of North Carolina Chapel Hill North Carolina USA
- Department of Chemistry University of North Carolina Chapel Hill North Carolina USA
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3
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Yousefi M, Rad MS, Shakibazadeh R, Ghodrati L, Kachoie MA. Simulating a heteroatomic CBN fullerene-like nanocage towards the drug delivery of fluorouracil. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2086252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Mohammad Yousefi
- Department of Chemistry, Faculty of Pharmaceutical Chemistry, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mehdi Salehi Rad
- Department of Chemistry, Yadegar-e Imam Khomeini (RAH) Shahr-e-Rey Branch, Islamic Azad University, Tehran, Iran
| | | | - Leila Ghodrati
- Department of Medicinal Plants, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Mehrdad Ataie Kachoie
- Department of Medicinal Plants, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
- Medicinal Plants Processing Center, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
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4
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Cao Y, Rajhi AA, Abedi M, Yousefi M, Choobak E. Coronene surface for delivery of Favipiravir: Computational approach. INORG CHEM COMMUN 2022. [DOI: 10.1016/j.inoche.2021.109133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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5
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Shteingolts SA, Stash AI, Tsirelson VG, Fayzullin RR. Orbital-Free Quantum Crystallographic View on Noncovalent Bonding: Insights into Hydrogen Bonds, π⋅⋅⋅π and Reverse Electron Lone Pair⋅⋅⋅π Interactions. Chemistry 2021; 27:7789-7809. [PMID: 33769620 DOI: 10.1002/chem.202005497] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Indexed: 01/16/2023]
Abstract
A detailed analysis of a complete set of the local potentials that appear in the Euler equation for electron density is carried out for noncovalent interactions in the crystal of a uracil derivative using experimental X-ray charge density. The interplay between the quantum theory of atoms in molecules and crystals and the local potentials and corresponding inner-crystal electronic forces of electrostatic and kinetic origin is explored. Partitioning of crystal space into atomic basins and atomic-like potential basins led us to the definite description of interatomic interaction and charge transfer. Novel physically grounded bonding descriptors derived within the orbital-free quantum crystallography provided the detailed examination of π-stacking and intricate C=O⋅⋅⋅π interactions and nonclassical hydrogen bonds present in the crystal. The donor-acceptor character of these interactions is revealed by analysis of Pauli and von Weizsäcker potentials together with well-known functions, e. g., deformation electron density and electron localization function. In this way, our analysis throws light on aspects of these closed-shell interactions hitherto hidden from the description.
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Affiliation(s)
- Sergey A Shteingolts
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
| | - Adam I Stash
- A.N. Nesmeyanov Institute of Organoelement Compounds Russian Academy of Sciences, 28 Vavilov Street, Moscow, 119991, Russian Federation
| | - Vladimir G Tsirelson
- D.I. Mendeleev University of Chemical Technology, 9 Miusskaya Square, Moscow, 125047, Russian Federation
| | - Robert R Fayzullin
- Arbuzov Institute of Organic and Physical Chemistry FRC Kazan Scientific Center, Russian Academy of Sciences, 8 Arbuzov Street, Kazan, 420088, Russian Federation
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6
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Li M, He X, Chen J, Wang B, Liu S, Rong C. Density Functional Theory and Information-Theoretic Approach Study on the Origin of Homochirality in Helical Structures. J Phys Chem A 2021; 125:1269-1278. [PMID: 33527833 DOI: 10.1021/acs.jpca.0c10310] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Homochirality of macromolecules such as proteins and DNA is one of the most striking features in nature; yet, there is still no convincing theory to explain its origin. In a recent work by one of the present authors (J. Phys. Chem. Lett. 2020, 11, 8690-8696), a general proposal from the viewpoint of thermodynamics has been put forward. It proposes that it is the handedness of helices ubiquitous in biological macromolecules that plays the decisive role. It also unveiled that there exist strong cooperativity effects dominated by favorable electrostatic interactions in the homochiral conformer. In this work, making use of analytical tools, we recently developed a density functional theory and an information-theoretic approach and through four sets of helical structures we designed for the present study, we examine these systems to provide new insights about these properties. We found that the 310-helix and the α-helix are markedly different in cooperativity from the viewpoint of both the total energy and its three components. The electrostatic dominance of homochiral species is manifested by both the electron charge distribution and information gain. At the atomic level, different elements behave significantly differently because they play different roles in the systems. Our results from this work validate that these analytical tools can be applied to homochiral systems, which can be further extended to others with potential interest in asymmetric synthesis and macromolecular assembly where the Principle of Homochirality Hierarchy comes into play.
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Affiliation(s)
- Meng Li
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Xin He
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Jie Chen
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Bin Wang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States
| | - Chunying Rong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China), Hunan Normal University, Changsha, Hunan 410081, P.R. China
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7
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Alipour M, Khorrami M. Pauli energy and information-theoretic approach for evaluating dynamic and nondynamic electron correlation. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-02689-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Matrodi A, Noorizadeh S. N-Derivatives of Shannon entropy density as response functions. Phys Chem Chem Phys 2020; 22:21535-21542. [PMID: 32959037 DOI: 10.1039/d0cp03808c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The exact first and second order partial derivatives of Shannon entropy density with respect to the number of electrons at constant external potential are introduced as new descriptors for prediction of the active sites of a molecule. The derivatives, which are a measure of the inhomogeneity of electron density, are calculated both exactly (from analytical forms) and approximately (using the finite difference method) for some molecular systems. According to the maximum entropy principle, the extreme value of the first order derivative on the surface of a given molecule should determine the active sites of the molecule in electrophilic and nucleophilic attack. The second order derivative indicates where the Shannon entropy is more concentrated or depleted during the electron exchange. Although these derivatives on the surfaces of helium and neon atoms are uniform, the corresponding values for argon, krypton and xenon atoms are not. This could explain the greater tendency of heavy noble gas atoms to form stable compounds. A dual descriptor is also defined as the difference between the left and right first order derivatives of Shannon entropy density, which allows one to simultaneously predict the preferable sites for electrophilic and nucleophilic attack over the system at point r. Therefore, the reactivity of an atom in a molecule requires the non-uniformity of the first and second order derivatives of Shannon entropy density on the surface of that atom.
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Affiliation(s)
- Abdolkarim Matrodi
- Chemistry Department, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
| | - Siamak Noorizadeh
- Chemistry Department, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
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9
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A comparative study to predict regioselectivity, electrophilicity and nucleophilicity with Fukui function and Hirshfeld charge. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2515-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Wu J, Yu D, Liu S, Rong C, Zhong A, Chattaraj PK, Liu S. Is It Possible To Determine Oxidation States for Atoms in Molecules Using Density-Based Quantities? An Information-Theoretic Approach and Conceptual Density Functional Theory Study. J Phys Chem A 2019; 123:6751-6760. [PMID: 31305075 DOI: 10.1021/acs.jpca.9b05054] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The oxidation state, also called oxidation number, of atoms in molecules is a fundamental chemical concept. It is defined as the charge of an atom in a molecule after the ionic approximation of its heteronuclear bonds is applied. Even though for simple molecules the assignment of oxidation states is straightforward, redundancy and ambiguity do exist for others. In this work, we present a density-based framework to determine the oxidation state using the quantities from the information-theoretic approach. As a proof of concept, we examined six elements for a total of 49 molecules. Strong linear correlations were obtained with Shannon entropy, Ghosh-Berkowitz-Parr entropy, information gain, relative Rényi entropy of orders 2 and 3, and Hirshfeld charge. We also discovered that the crystal radius of elements plays the key role in rationalizing the system dependent nature of these strong linear correlations. The validity and effectiveness of our results were demonstrated by the examples of molecules containing elements with two or more oxidation states. Our results should be applicable to more complicated systems in assigning different oxidation states.
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Affiliation(s)
- Jingyi Wu
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha , Hunan 410081 , P.R. China
| | - Donghai Yu
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha , Hunan 410081 , P.R. China
| | - Siyuan Liu
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha , Hunan 410081 , P.R. China
| | - Chunying Rong
- College of Chemistry and Chemical Engineering , Hunan Normal University , Changsha , Hunan 410081 , P.R. China
| | - Aiguo Zhong
- School of Pharmaceutical and Chemical Engineering , Taizhou University , 1139 Shifu Road , Linhai , Zhejiang 318000 , P.R. China
| | - Pratim K Chattaraj
- Department of Chemistry and Center for Theoretical Studies , Indian Institute of Technology , Kharagpur 721302 , India
| | - Shubin Liu
- Research Computing Center , University of North Carolina , Chapel Hill , North Carolina 27599-3420 , United States
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11
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Rincon L, Javier Torres F, Becerra M, Liu S, Fritsch A, Almeida R. On the separation of the information content of the Fermi and Coulomb holes and their influence on the electronic properties of molecular systems. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1530462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Luis Rincon
- Grupo de Química Computacional y Teórica (QCT-USFQ) and Instituto de Simulación Computacional (ISC-USFQ), Dept. de Ingeniería Química, Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito, Quito, Ecuador
- Departamento de Química, Facultad de Ciencias, Universidad de Los Andes (ULA), Mérida, Venezuela
| | - F. Javier Torres
- Grupo de Química Computacional y Teórica (QCT-USFQ) and Instituto de Simulación Computacional (ISC-USFQ), Dept. de Ingeniería Química, Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito, Quito, Ecuador
| | - Marcos Becerra
- Grupo de Química Computacional y Teórica (QCT-USFQ) and Instituto de Simulación Computacional (ISC-USFQ), Dept. de Ingeniería Química, Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito, Quito, Ecuador
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, NC, USA
| | - Alain Fritsch
- Institut des Sciences Molèculaires, Theoretical Chemistry & Modeling Group, Universitè Bordeaux, Talance, France
| | - Rafael Almeida
- Departamento de Química, Facultad de Ciencias, Universidad de Los Andes (ULA), Mérida, Venezuela
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12
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13
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Alipour M, Badooei Z. Toward Electron Correlation and Electronic Properties from the Perspective of Information Functional Theory. J Phys Chem A 2018; 122:6424-6437. [DOI: 10.1021/acs.jpca.8b05703] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mojtaba Alipour
- Department of Chemistry, College of Sciences, Shiraz University, Shiraz 71946-84795, Iran
| | - Zeinab Badooei
- Department of Chemistry, College of Sciences, Shiraz University, Shiraz 71946-84795, Iran
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14
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15
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16
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17
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18
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Rincón L, Almeida R, Contreras PL, Javier Torres F. The information content of the conditional pair probability. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.06.053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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19
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Lin CH, Ho YK. Shannon information entropy in position space for two-electron atomic systems. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.05.029] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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20
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Rong C, Lu T, Ayers PW, Chattaraj PK, Liu S. Scaling properties of information-theoretic quantities in density functional reactivity theory. Phys Chem Chem Phys 2015; 17:4977-88. [DOI: 10.1039/c4cp05609d] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A number of strong linear correlations between information-theoretic quantities and electron populations for atoms, molecules, and atoms-in-molecules have been disclosed.
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Affiliation(s)
- Chunying Rong
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China)
- College of Chemistry and Chemical Engineering
- Hunan Normal University
- Changsha Hunan 410081
- China
| | - Tian Lu
- Beijing Kein Research Center for Natural Sciences
- Beijing 100022
- P. R. China
| | - Paul W. Ayers
- Department of Chemistry
- McMaster University
- Hamilton
- Canada
| | - Pratim K. Chattaraj
- Department of Chemistry and Center for Theoretical Studies
- Indian Institute of Technology
- Kharagpur 721302
- India
| | - Shubin Liu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research (Ministry of Education of China)
- College of Chemistry and Chemical Engineering
- Hunan Normal University
- Changsha Hunan 410081
- China
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21
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Stash AI, Tsirelson VG. DevelopingWinXPRO: a software for determination of the multipole-model-based properties of crystals. J Appl Crystallogr 2014. [DOI: 10.1107/s1600576714021566] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The new release of the computer program packageWinXPRO v.3xfor determination of the crystal properties from parameters of the multipole-modeled experimental electron density and anharmonic atomic displacement coefficients is described. The set of properties is significantly extended by using the density functional and information theories. In addition, a built-in multi-functional viewer and programs to display the output data, including the mapping of the chosen functional bonding descriptors onto surfaces of the other properties, are included.
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22
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Oliveira BG. The structures of heterocyclic complexes ruled by hydrogen bonds and halogen interactions: interaction strength and IR modes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 124:208-215. [PMID: 24486864 DOI: 10.1016/j.saa.2013.12.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 11/22/2013] [Accepted: 12/04/2013] [Indexed: 06/03/2023]
Abstract
In this work, the existence of multiple interactions in heterocyclic complexes of C2H4O⋯nHCCl3 and C2H4S⋯nHCCl3 with n=2 and 3 was unveiled at the B3LYP/6-311++G(d,p) level of theory. The forward analyses of the vibrational spectra revealed the appearing of red-shifts in the H-C bond. In agreement with this and through the optimized geometries of these systems, an increase in the H-C bond length was also observed. Besides O⋯H and S⋯H, other hydrogen bonds formed between chlorine⋯hydrogen and mainly the halogen interactions formed by chlorine⋯chlorine were identified. Thereby, the vibration spectra of the heterocyclic complexes were reanalyzed with the purpose to locate new red-shifts, although only those characterized in H-C have been detected up to then. In addition to the correlation between the frequencies shifted to downward values followed by increases in the bond lengths, the interpretation of the red-shifts was conducted by means of the Bent rule of the hybridization theory. The interaction strength was examined in several viewpoints, and one of them was the relationship between the H-bond energies and the intermolecular electronic density computed by means of the Quantum Theory of Atoms in Molecules (QTAIM). Moreover, the prediction of the interaction strength was also made through the combination between vibration modes (red-shifts) and variation of topological parameters, such as the electronic density and Laplacian of the proton donor bond (C-H).
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Affiliation(s)
- Boaz G Oliveira
- Institute of Environmental Sciences and Sustainable Development (ICADS), Federal University of Bahia, 47801-100 Barreiras, BA, Brazil.
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23
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Oliveira BGD. Structure, energy, vibrational spectrum, and Bader's analysis of π⋯H hydrogen bonds and H−δ⋯H+δdihydrogen bonds. Phys Chem Chem Phys 2013; 15:37-79. [DOI: 10.1039/c2cp41749a] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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24
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Alipour M, Mohajeri A. Onicescu information energy in terms of Shannon entropy and Fisher information densities. Mol Phys 2012. [DOI: 10.1080/00268976.2011.649795] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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