Electron Density, Interaction Energy and Hydrogen-Bond Radius of C–H...O Interaction

In the presented research, we address the original concept of resonance-assisted hydrogen bonding (RAHB) by means of the many-body interaction approach and electron density delocalization analysis. The investigated molecular patterns of RAHBs are open chains consisting of two to six molecules in which the intermolecular hydrogen bond stabilizes the complex. Non-RAHB counterparts are considered to be reference systems. The results show the influence of the neighbour monomers on the unsaturated chains in terms of the many-body interaction energy contribution. Exploring the relation between the energy parameters and the growing number of molecules in the chain, we give an explicit extrapolation of the interaction energy and its components in the infinite chain. Electron delocalization within chain motifs has been analysed from three different points of view: three-body delocalization between C=C-C, two-body hydrogen bond delocalization indices and also between fragments (monomers). A many-body contribution to the interaction energy as well as electron density helps to establish the assistance of resonance in the strength of hydrogen bonds upon the formation of the present molecular chains. The direct relation between interaction energy and delocalization supports the original concept, and refutes some of the criticisms of the RAHB idea.

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Exploring the rare S—H...S hydrogen bond using charge density analysis in isomers of mercaptobenzoic acid

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520617008344 ◽

2017 ◽

Vol 73 (4) ◽

pp. 626-633 ◽

Cited By ~ 5

Author(s):

Mysore. S Pavan ◽

Sounak Sarkar ◽

Tayur N. Guru Row

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonding ◽

Charge Density ◽

Interaction Energy ◽

Electron Density ◽

Type I ◽

Weak Hydrogen Bond ◽

Topological Features ◽

Density Analysis ◽

Density Study

Experimental and theoretical charge density analyses on isomers of mercaptobenzoic acid have been carried out to quantify the hydrogen bonding of the hitherto less explored thiols, to assess the strength of the interactions using the topological features of the electron density. The electron density study offers interesting insights into the nature of the S—H...S interaction. The interaction energy is comparable with that of a weak hydrogen bond. The strength and directionality of the S—H...S hydrogen bond is demonstrated to be mainly due to the conformation locking potential of the intramolecular S...O chalcogen bond in 2-mercaptobenzoic acid and is stronger than in 3-mercaptobenzoic acid, which lacks the intramolecular S...O bond. Thepara-substituted mercaptobenzoic acid depicts a type I S...S interaction.

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Relationships between Interaction Energy and Electron Density Properties for Homo Halogen Bonds of the [(A)nY–X···X–Z(B)m] Type (X = Cl, Br, I)

Molecules ◽

10.3390/molecules24152733 ◽

2019 ◽

Vol 24 (15) ◽

pp. 2733 ◽

Cited By ~ 6

Author(s):

Maxim L. Kuznetsov

Keyword(s):

Kinetic Energy ◽

Interaction Energy ◽

Electron Density ◽

Bond Critical Point ◽

Kinetic Energy Density ◽

Large Set ◽

Halogen Bonds ◽

Absolute Deviation ◽

The Individual ◽

Best Estimator

Relationships between interaction energy (Eint) and electron density properties at the X···X bond critical point or the d(X···X) distance were established for the large set of structures [(A)nY–X···X–Z(B)m] bearing the halogen bonds Cl···Cl, Br···Br, and I···I (640 structures in total). The best estimator of Eint is the kinetic energy density (Gb), which reasonably approximates the whole set of the structures as −Eint = 0.128Gb2 − 0.82Gb + 1.66 (R2 = 0.91, mean absolute deviation 0.39 kcal/mol) and demonstrates low dispersion. The potential and kinetic energy densities, electron density, and the d(X···X) distance behave similarly as estimators of Eint for the individual series Cl···Cl, Br···Br, and I···I. A number of the Eint(property) correlations are recommended for the practical application in the express estimates of the strength of the homo-halogen bonds.

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Theoretical study of electron structure and stability of quasiaromatic analogues of azulene

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19810031 ◽

1981 ◽

Vol 46 (1) ◽

pp. 31-39 ◽

Cited By ~ 1

Author(s):

Pavol Zahradník ◽

Elena Ďurčíková ◽

Jaroslav Leška

Keyword(s):

Hydrogen Bond ◽

Interaction Energy ◽

Theoretical Study ◽

Electron System ◽

Stabilization Energy ◽

Strong Hydrogen Bond ◽

Hydrogen Bridge ◽

Structure And Stability ◽

Energy Interaction ◽

The Stability

Semiempirical CNDO/2 method was used in the study of 23 quasiaromatic azulene analogues containing a hydrogen bridge A..H-D, where A and D denote O, NH, or S. The values of the stabilization energy, interaction energy, and changes of Wiberg's indexes suggest that the stability of the studied compounds is caused by a strong hydrogen bond as well as by a strong delocalization of the π-electron system. Derivatives in which A and D are O and NH are especially stable. Derivatives containing an oxo or thio group are preferred in tautomeric equilibriums.

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Fast analytical evaluation of intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density. III. Application to crystal structures via the Ewald and direct summation methods

Acta Crystallographica Section A Foundations and Advances ◽

10.1107/s2053273320009584 ◽

2020 ◽

Vol 76 (6) ◽

pp. 630-651

Author(s):

Daniel Nguyen ◽

Piero Macchi ◽

Anatoliy Volkov

Keyword(s):

Interaction Energy ◽

Crystal Structures ◽

Electron Density ◽

Small Molecule ◽

Electrostatic Interaction ◽

Multipole Moment ◽

Interaction Energies ◽

Acta Cryst ◽

Löwdin Α Function ◽

Direct Summation

The previously reported exact potential and multipole moment (EP/MM) method for fast and accurate evaluation of the intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density [Volkov, Koritsanszky & Coppens (2004). Chem. Phys. Lett. 391, 170–175; Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524–536; Nguyen & Volkov (2019). Acta Cryst. A75, 448–464] is extended to the calculation of electrostatic interaction energies in molecular crystals using two newly developed implementations: (i) the Ewald summation (ES), which includes interactions up to the hexadecapolar level and the EP correction to account for short-range electron-density penetration effects, and (ii) the enhanced EP/MM-based direct summation (DS), which at sufficiently large intermolecular separations replaces the atomic multipole moment approximation to the electrostatic energy with that based on the molecular multipole moments. As in the previous study [Nguyen, Kisiel & Volkov (2018). Acta Cryst. A74, 524–536], the EP electron repulsion integral is evaluated analytically using the Löwdin α-function approach. The resulting techniques, incorporated in the XDPROP module of the software package XD2016, have been tested on several small-molecule crystal systems (benzene, L-dopa, paracetamol, amino acids etc.) and the crystal structure of a 181-atom decapeptide molecule (Z = 4) using electron densities constructed via the University at Buffalo Aspherical Pseudoatom Databank [Volkov, Li, Koritsanszky & Coppens (2004). J. Phys. Chem. A, 108, 4283–4300]. Using a 2015 2.8 GHz Intel Xeon E3-1505M v5 computer processor, a 64-bit implementation of the Löwdin α-function and one of the higher optimization levels in the GNU Fortran compiler, the ES method evaluates the electrostatic interaction energy with a numerical precision of at least 10−5 kJ mol−1 in under 6 s for any of the tested small-molecule crystal structures, and in 48.5 s for the decapeptide structure. The DS approach is competitive in terms of precision and speed with the ES technique only for crystal structures of small molecules that do not carry a large molecular dipole moment. The electron-density penetration effects, correctly accounted for by the two described methods, contribute 28–64% to the total electrostatic interaction energy in the examined systems, and thus cannot be neglected.

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Electron-density-based calculations of intermolecular energy: case of urea

Acta Crystallographica Section A Foundations of Crystallography ◽

10.1107/s0108767399001993 ◽

1999 ◽

Vol 55 (5) ◽

pp. 821-827 ◽

Cited By ~ 18

Author(s):

Kyrill Yu. Suponitsky ◽

Vladimir G. Tsirelson ◽

Dirk Feil

Keyword(s):

Interaction Energy ◽

Electron Density ◽

Theoretical Data ◽

Multipole Moments ◽

Intermolecular Interaction Energy ◽

Hartree Fock ◽

Intermolecular Energy ◽

Crystalline Urea ◽

To Come ◽

Experimental Values

The intermolecular interaction energy in crystalline urea has been calculated both from diffraction data and from the Hartree–Fock crystalline electron-density distribution, using a modified atom–atom approximation scheme. The electrostatic part of this energy has been calculated from the atomic multipole moments, obtained by adjustment of the multipole model to experimental X-ray and to theoretical Hartree–Fock structure amplitudes. To obtain the induction energy, multipole moments were calculated from structure amplitudes for the crystalline electron density and from those that refer to the electron density of a superposition of isolated molecules. This worked well for the calculation of the interaction energy from Hartree–Fock data (6% difference from the sublimation-energy value), but not for the interaction energy from experimental data, where the moments of the superposition have to come from Hartree–Fock calculations: the two sets of multipole moments are far too different. The uncertainty of the phases of the structure amplitudes, combined with systematic errors in the theoretical data and noise in the experimental values, may account for the discrepancies. The nature of the different contributions to intermolecular interactions for urea is examined.

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