12 results on '"Source function"'
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2. The explicit role of electron exchange in the hydrogen bonded molecular complexes.
- Author
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Levina, Elena O., Khrenova, Maria G., and Tsirelson, Vladimir G.
- Subjects
- *
CHEMICAL bonds , *ELECTRON density , *BINDING energy , *ELECTRONS , *ELECTRON delocalization , *CRITICAL point (Thermodynamics) , *HYDROGEN bonding - Abstract
We applied a set of advanced bonding descriptors to establish the hidden electron density features and binding energy characteristics of intermolecular DH∙∙∙A hydrogen bonds (OH∙∙∙O, NH∙∙∙O and SH∙∙∙O) in 150 isolated and solvated molecular complexes. The exchange‐correlation and Pauli potentials as well as corresponding local one‐electron forces allowed us to explicitly ascertain how electron exchange defines the bonding picture in the proximity of the H‐bond critical point. The electron density features of DH∙∙∙A interaction are governed by alterations in the electron localization in the H‐bond region displaying itself in the exchange hole. At that, they do not depend on the variations in the exchange hole mobility. The electrostatic interaction mainly defines the energy of H‐bonds of different types, whereas the strengthening/weakening of H‐bonds in complexes with varying substituents depends on the barrier height of the exchange potential near the bond critical point. Energy variations between H‐bonds in isolated and solvated systems are also caused the electron exchange peculiarities as follows from the corresponding potential and the interacting quantum atom analyses complemented by electron delocalization index calculations. Our approach is based on the bonding descriptors associated with the characteristics of the observable electron density and can be recommended for in‐depth studies of non‐covalent bonding. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
3. When does a hydrogen bond become a van der Waals interaction? a topological answer.
- Author
-
Tantardini, Christian
- Subjects
- *
HYDROGEN bonding , *VAN der Waals forces , *MOLECULAR interactions , *QUANTUM theory of the atom , *ELECTRONIC structure - Abstract
The hydrogen bond (H‐bond) is among the most important noncovalent interaction (NCI) for bioorganic compounds. However, no "energy border" has yet been identified to distinguish it from van der Waals (vdW) interaction. Thus, classifying NCIs and interpreting their physical and chemical importance remain open to great subjectivity. In this work, the "energy border" between vdW and H‐bonding interactions was identified using a dimer of water, as well as for a series of classical and nonclassical H‐bonding systems. Through means of the quantum theory of atoms in molecules and in particular the source function, it was possible to clearly identify the transition from H‐bonding to vdW bonding via analysis of the electronic structure. This "energy border" was identified both on elongating the interatomic interaction and by varying the contact angle. Hence, this study also redefines the "critic angle" previously proposed by Galvão et al. (J. Phys. Chem. A 2013, 117, 12668). Consequently, such "energy border" through an analysis of atomic basins volume variation was possible to identify the end of long‐range interactions. © 2019 Wiley Periodicals, Inc. The topological tool source function calculated at the bond critical point of CS dimer of water subjected to variation of angle with the fulcra in the hydrogen (H) between H‐donor (D) and the H‐acceptor (A) oxygen atoms θ(D − H⋯A) and a variation of A⋯D distance (RA⋯D) allowed to define the border between hydrogen bond (H‐bond) and van der Waals. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
4. An Electron Density Source‐Function Study of DNA Base Pairs in Their Neutral and Ionized Ground States†.
- Author
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Gatti, Carlo, Macetti, Giovanni, Boyd, Russell J., and Matta, Chérif F.
- Subjects
- *
ELECTRON density , *GROUND state (Quantum mechanics) , *GREEN'S functions , *CHEMICAL bonds , *COMPUTATIONAL chemistry - Abstract
The source function (SF) decomposes the electron density at any point into contributions from all other points in the molecule, complex, or crystal. The SF “illuminates” those regions in a molecule that most contribute to the electron density at a point of reference. When this point of reference is the bond critical point (BCP), a commonly used surrogate of chemical bonding, then the SF analysis at an atomic resolution within the framework of Bader's Quantum Theory of Atoms in Molecules returns the contribution of each atom in the system to the electron density at that BCP. The SF is used to locate the important regions that control the hydrogen bonds in both Watson–Crick (WC) DNA dimers (adenine:thymine (AT) and guanine:cytosine (GC)) which are studied in their neutral and their singly ionized (radical cationic and anionic) ground states. The atomic contributions to the electron density at the BCPs of the hydrogen bonds in the two dimers are found to be delocalized to various extents. Surprisingly, gaining or loosing an electron has similar net effects on some hydrogen bonds concealing subtle compensations traced to atomic sources contributions. Coarser levels of resolutions (groups, rings, and/or monomers‐in‐dimers) reveal that distant groups and rings often have non‐negligible effects especially on the weaker hydrogen bonds such as the third weak CH⋅⋅⋅O hydrogen bond in AT. Interestingly, neither the purine nor the pyrimidine in the neutral or ionized forms dominate any given hydrogen bond despite that the former has more atoms that can act as source or sink for the density at its BCP. © 2018 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
5. An Electron Density Source‐Function Study of DNA Base Pairs in Their Neutral and Ionized Ground States†.
- Author
-
Gatti, Carlo, Macetti, Giovanni, Boyd, Russell J., and Matta, Chérif F.
- Subjects
ELECTRON density ,GROUND state (Quantum mechanics) ,GREEN'S functions ,CHEMICAL bonds ,COMPUTATIONAL chemistry - Abstract
The source function (SF) decomposes the electron density at any point into contributions from all other points in the molecule, complex, or crystal. The SF “illuminates” those regions in a molecule that most contribute to the electron density at a point of reference. When this point of reference is the bond critical point (BCP), a commonly used surrogate of chemical bonding, then the SF analysis at an atomic resolution within the framework of Bader's Quantum Theory of Atoms in Molecules returns the contribution of each atom in the system to the electron density at that BCP. The SF is used to locate the important regions that control the hydrogen bonds in both Watson–Crick (WC) DNA dimers (adenine:thymine (AT) and guanine:cytosine (GC)) which are studied in their neutral and their singly ionized (radical cationic and anionic) ground states. The atomic contributions to the electron density at the BCPs of the hydrogen bonds in the two dimers are found to be delocalized to various extents. Surprisingly, gaining or loosing an electron has similar net effects on some hydrogen bonds concealing subtle compensations traced to atomic sources contributions. Coarser levels of resolutions (groups, rings, and/or monomers‐in‐dimers) reveal that distant groups and rings often have non‐negligible effects especially on the weaker hydrogen bonds such as the third weak CH⋅⋅⋅O hydrogen bond in AT. Interestingly, neither the purine nor the pyrimidine in the neutral or ionized forms dominate any given hydrogen bond despite that the former has more atoms that can act as source or sink for the density at its BCP. © 2018 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
6. Spin density accuracy and distribution in azido Cu(II) complexes: A source function analysis.
- Author
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Macetti, Giovanni, Lo Presti, Leonardo, and Gatti, Carlo
- Subjects
- *
AZIDO group , *COPPER compounds , *NUCLEAR spin , *ELECTRON density , *FERROMAGNETIC materials - Abstract
Magnetic properties of open‐shell systems depend on their unpaired electron density distribution. Accurate spin density (SD) is difficult to retrieve, both from polarized neutron diffraction (PND) data and from quantum approaches, and its interpretation is not trivial. The Source Function is a useful tool to interpret SD distributions and their accuracy. It is here applied to analyze and compare the theoretical SD in a weakly ferromagnetically coupled end‐end azido dicopper complex with that in a strongly‐coupled end‐on complex. The Source Function enables to highlight the origin of the SD differences between the two dicopper complexes and among adopted computational approaches (CASSCF, DFT, UHF). Further insight is provided by partial Source Function SD reconstructions using given subsets of atoms. DFT methods exaggerate electron sharing between copper and the ligands, causing spin delocalization toward them and overestimating metal‐ligand spin polarization, while underestimating CASSCF spin information transmission between atoms. CAS(10,10) SD is closer to the PND SD than other adopted methods © 2018 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
7. Source function and plane waves: Toward complete bader analysis.
- Author
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Tantardini, Christian, Ceresoli, Davide, and Benassi, Enrico
- Subjects
- *
GREEN'S functions , *ELECTRON density , *PLANE wavefronts - Abstract
The source function (SF) is a topological descriptor that was introduced and developed by C. Gatti and R.W. Bader in 1998. The SF describes the contribution of each atom to the total electron density at a given point. To date, this descriptor has only been calculable from electron densities generated by all-electron (AE) methods for the investigation of single molecules or periodic systems. This study broadens the accessibility of the SF, offering its calculation from electron densities generated by plane wave (PW) methods. The new algorithm has been implemented in the open source code, CRITIC2. Our novel approach has been validated on a series of test systems, comparing the results obtained at PW level with those previously obtained through AE methods. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
8. An Electron Density Source-Function Study of DNA Base Pairs in Their Neutral and Ionized Ground States†
- Author
-
Carlo Gatti, Chérif F. Matta, Giovanni Macetti, and Russell J. Boyd
- Subjects
Electron density ,Electrons ,Source Function ,Electron ,010402 general chemistry ,01 natural sciences ,Hydrogen bonds ,Delocalized electron ,0103 physical sciences ,Atom ,Charge density topology ,Molecule ,Base Pairing ,DNA pairs ,010304 chemical physics ,Hydrogen bond ,Chemistry ,Atoms in molecules ,Hydrogen Bonding ,DNA ,General Chemistry ,0104 chemical sciences ,Computational Mathematics ,Chemical bond ,Chemical physics ,Quantum Theory - Abstract
The source function (SF) decomposes the electron density at any point into contributions from all other points in the molecule, complex, or crystal. The SF "illuminates" those regions in a molecule that most contribute to the electron density at a point of reference. When this point of reference is the bond critical point (BCP), a commonly used surrogate of chemical bonding, then the SF analysis at an atomic resolution within the framework of Bader's Quantum Theory of Atoms in Molecules returns the contribution of each atom in the system to the electron density at that BCP. The SF is used to locate the important regions that control the hydrogen bonds in both Watson-Crick (WC) DNA dimers (adenine:thymine (AT) and guanine:cytosine (GC)) which are studied in their neutral and their singly ionized (radical cationic and anionic) ground states. The atomic contributions to the electron density at the BCPs of the hydrogen bonds in the two dimers are found to be delocalized to various extents. Surprisingly, gaining or loosing an electron has similar net effects on some hydrogen bonds concealing subtle compensations traced to atomic sources contributions. Coarser levels of resolutions (groups, rings, and/or monomers-in-dimers) reveal that distant groups and rings often have non-negligible effects especially on the weaker hydrogen bonds such as the third weak CH⋅⋅⋅O hydrogen bond in AT. Interestingly, neither the purine nor the pyrimidine in the neutral or ionized forms dominate any given hydrogen bond despite that the former has more atoms that can act as source or sink for the density at its BCP. © 2018 Wiley Periodicals, Inc.
- Published
- 2018
- Full Text
- View/download PDF
9. Source function and plane waves: Toward complete bader analysis
- Author
-
Davide Ceresoli, Enrico Benassi, and Christian Tantardini
- Subjects
Source function ,Electron density ,Series (mathematics) ,Chemistry ,Plane wave ,02 engineering and technology ,General Chemistry ,Electron ,021001 nanoscience & nanotechnology ,01 natural sciences ,Computational physics ,Computational Mathematics ,Open source ,Computational chemistry ,0103 physical sciences ,Atom ,Point (geometry) ,010306 general physics ,0210 nano-technology - Abstract
The source function (SF) is a topological descriptor that was introduced and developed by C. Gatti and R.W. Bader in 1998. The SF describes the contribution of each atom to the total electron density at a given point. To date, this descriptor has only been calculable from electron densities generated by all-electron (AE) methods for the investigation of single molecules or periodic systems. This study broadens the accessibility of the SF, offering its calculation from electron densities generated by plane wave (PW) methods. The new algorithm has been implemented in the open source code, CRITIC2. Our novel approach has been validated on a series of test systems, comparing the results obtained at PW level with those previously obtained through AE methods. © 2016 Wiley Periodicals, Inc.
- Published
- 2016
- Full Text
- View/download PDF
10. Spin density accuracy and distribution in azido Cu(II) complexes: A source function analysis
- Author
-
Giovanni Macetti, Carlo Gatti, and Leonardo Lo Presti
- Subjects
Physics ,Source function ,010304 chemical physics ,Spin polarization ,Neutron diffraction ,spin density topology source function ,General Chemistry ,Electron ,010402 general chemistry ,01 natural sciences ,Molecular physics ,0104 chemical sciences ,Computational Mathematics ,Delocalized electron ,Unpaired electron ,0103 physical sciences ,Quantum ,Spin-½ - Abstract
Magnetic properties of open-shell systems depend on their unpaired electron density distribution. Accurate spin density (SD) is difficult to retrieve, both from polarized neutron diffraction (PND) data and from quantum approaches, and its interpretation is not trivial. The Source Function is a useful tool to interpret SD distributions and their accuracy. It is here applied to analyze and compare the theoretical SD in a weakly ferromagnetically coupled end-end azido dicopper complex with that in a strongly-coupled end-on complex. The Source Function enables to highlight the origin of the SD differences between the two dicopper complexes and among adopted computational approaches (CASSCF, DFT, UHF). Further insight is provided by partial Source Function SD reconstructions using given subsets of atoms. DFT methods exaggerate electron sharing between copper and the ligands, causing spin delocalization toward them and overestimating metal-ligand spin polarization, while underestimating CASSCF spin information transmission between atoms. CAS(10,10) SD is closer to the PND SD than other adopted methods © 2018 Wiley Periodicals, Inc.
- Published
- 2017
- Full Text
- View/download PDF
11. Chemical information from the source function
- Author
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Luca Bertini, Carlo Gatti, Fausto Cargnoni, Gatti, C, Cargnoni, F, and Bertini, L
- Subjects
Hydrogen bond ,Source function ,Electron density ,education.field_of_study ,Chemistry ,Population ,General Chemistry ,Topology ,Diatomic molecule ,Electron localization function ,Critical point (mathematics) ,source function ,electron density ,hydrogen bond ,transferability ,topology ,Electronegativity ,Computational Mathematics ,Transferability ,Atom ,Atomic physics ,education - Abstract
The source function, which enables one to equate the value of the electron density at any point within a molecule to a sum of atomic contributions, has been applied to a number of cases. The source function is a model-independent, quantitative measure of the relative importance of an atom's or group's contribution to the density at any point in a system, and it represents a potentially interesting tool to provide chemical information. It is shown that the source contribution from H to the electron density rho(b) at the bond critical point in HX diatomics decreases with increasing X's electronegativity, and that this decrease is a result of significant changes in the Laplacian distribution within the H-basin. It is also demonstrated that the source function from Li to rho(b) in LiX diatomics is a more sensitive index of atomic transferability than it is the lithium atomic energy or population. The observed changes are such as to ensure a constant percentage source contribution from Li to rho(b) throughout the LiX series, rather than a constant source as one would expect in the limit of perfect atomic transferability. Application of the source function to planar lithium clusters has revealed that the source function clearly discriminates between a nonnuclear electron density maximum and a maximum associated to a nucleus, on the basis of the relative weight of the source contributions from the basin associated to the maximum and from the remaining basins in the cluster. The source function has also allowed for a classification of hydrogen bonds in terms of characteristic source contributions to the density at the H-bond critical point from the H involved in the H-bond, the H-donor D, and the H-acceptor A. The source contribution from the H appears as the most distinctive marker of the H-bond strength, being highly negative for isolated H-bonds, slightly negative for polarized assisted H-bonds, close to zero for resonance-assisted H-bonds, and largely positive for charge-assisted H-bonds. The contributions from atoms other than H, D, and A strongly increase with decreasing H-bond strength, consistently with the parallel increased electrostatic character of the interaction. The correspondence between the classification provided by the Electron Localization Function topologic approach and by the source function has been highlighted. It is concluded that the source function represents a practical tool to disclose the local and nonlocal character of the electron density distributions and to quantify such a locality and nonlocality in terms of a physically sound and appealing chemical partitioning.
- Published
- 2003
- Full Text
- View/download PDF
12. An Electron Density Source-Function Study of DNA Base Pairs in Their Neutral and Ionized Ground States † .
- Author
-
Gatti C, Macetti G, Boyd RJ, and Matta CF
- Subjects
- Hydrogen Bonding, Base Pairing, DNA chemistry, Electrons, Quantum Theory
- Abstract
The source function (SF) decomposes the electron density at any point into contributions from all other points in the molecule, complex, or crystal. The SF "illuminates" those regions in a molecule that most contribute to the electron density at a point of reference. When this point of reference is the bond critical point (BCP), a commonly used surrogate of chemical bonding, then the SF analysis at an atomic resolution within the framework of Bader's Quantum Theory of Atoms in Molecules returns the contribution of each atom in the system to the electron density at that BCP. The SF is used to locate the important regions that control the hydrogen bonds in both Watson-Crick (WC) DNA dimers (adenine:thymine (AT) and guanine:cytosine (GC)) which are studied in their neutral and their singly ionized (radical cationic and anionic) ground states. The atomic contributions to the electron density at the BCPs of the hydrogen bonds in the two dimers are found to be delocalized to various extents. Surprisingly, gaining or loosing an electron has similar net effects on some hydrogen bonds concealing subtle compensations traced to atomic sources contributions. Coarser levels of resolutions (groups, rings, and/or monomers-in-dimers) reveal that distant groups and rings often have non-negligible effects especially on the weaker hydrogen bonds such as the third weak CH⋅⋅⋅O hydrogen bond in AT. Interestingly, neither the purine nor the pyrimidine in the neutral or ionized forms dominate any given hydrogen bond despite that the former has more atoms that can act as source or sink for the density at its BCP. © 2018 Wiley Periodicals, Inc., (© 2018 Wiley Periodicals, Inc.)
- Published
- 2018
- Full Text
- View/download PDF
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