Description of halogen bonding on the basis of multicenter multipole expansion

Titov, O. I.; Shulga, Dmitry A.; Palyulin, V. A.; Зефиров, Н. С.

doi:10.1134/s0012500813050042

Cited by 10 publications

(11 citation statements)

References 12 publications

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“…According to our previous analysis,18 there are two pertinent ways to describe halogen bonding in molecular mechanics: by means of extra‐point atom charges and by means of atomic multipoles (Figure 2). To select the approach best suited for our goal both models were built and compared on the large set of fragment‐like molecules.…”

Section: Methodsmentioning

confidence: 99%

“…Different ways of describing XB within a molecular mechanics force field framework have been proposed to date, the essential feature of each being the anisotropic electrostatic description in the vicinity of heavy halogen atoms. The latter is achieved by one of the two methods: with the use of extra‐point (EP) charges13–17 or multipole expansion‐based (ME) approaches 18–20. The EP techniques introduce an off‐atom positive point charge on the elongation of CX bond to create the desirable attraction between halogen and Lewis base, while the ME methods take advantage of multicenter multipole expansion for the same purpose.…”

Section: Introductionmentioning

confidence: 99%

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Perspectives of Halogen Bonding Description in Scoring Functions and QSAR/QSPR: Substituent Effects in Aromatic Core

Titov

Shulga

Palyulin

et al. 2015

Molecular Informatics

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Halogen bonding (XB) is a new promising interaction pattern in medicinal chemistry. It has predominantly electrostatic nature - high electrostatic potential anisotropy. However to fully unleash the potential of XB in rational drug design fast and robust empirical methods of XB description should be developed. Current approaches rely heavily on ab initio calculation for each molecule studied. Thus fast prediction of electrostatic parameters for description of XB for arbitrary organic molecules is of paramount importance to promptly establish QSAR/QSPR, virtual screening and molecular docking pipelines suitable for today's agile development requirements. The two most promising approaches to describe anisotropic electrostatic models - the extra point (EP) charge model and the multipole expansion (ME) model - were studied on their ability (1) to describe ab initio molecular electrostatic potential (MEP) and (2) to produce parameters that can be predicted for each molecule empirically rather than estimated via ab initio calculations. The reference ab initio MEP was calculated for a set of 730 substituted halobenzenes. Parameters for anisotropic electrostatics of both empirical models (EP and ME) studied were extracted from ab initio MEP. The FreeWilson and Hansch type QSPR models relating XB parameters with aromatic substituents were built and analyzed, providing the guidelines for further development.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Perspectives of Halogen Bonding Description in Scoring Functions and QSAR/QSPR: Substituent Effects in Aromatic Core

Titov

Shulga

Palyulin

et al. 2015

Molecular Informatics

View full text Add to dashboard Cite

show abstract

“…To describe the anisotropic nature of nonbonding interactions of the halogen atom, one has to move beyond the atomic charges and isotropic vdW radii. Although some authors introduced vdW repulsion anisotropy to predict the crystal structures, others argue that the anisotropy of electrostatic interactions is sufficient and propose adding atomic-centered dipole and quadrupole moments . Here, we adopt the latter approach, as implemented in AMOEBA FF .…”

Section: Introductionmentioning

confidence: 99%

“…Although some authors introduced vdW repulsion anisotropy to predict the crystal structures, 44 others argue that the anisotropy of electrostatic interactions is sufficient and propose adding atomic-centered dipole and quadrupole moments. 45 Here, we adopt the latter approach, as implemented in AMOEBA FF. 46 We use quantum chemistry data to improve the vdW parameters for I atoms in Section 3.1.…”

Section: Introductionmentioning

confidence: 99%

First-Principles Crystal Engineering of Nonlinear Optical Materials. II. Effect of Halogen Bonds on the Structure and Properties of Triiodobenzenes

et al. 2018

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Recently, we proposed a computational design strategy for organic nonlinear optical materials, based on the global minimization of lattice energy to predict the crystal packing from the first principles. Here, we validate this strategy on triiodobenzenes, which include CH···I hydrogen and I···I halogen bonding as the structure-determining components of their intermolecular interactions. To refine the van der Waals (vdW) parameters for an I atom, the ab initio potential surfaces for the model dimers were calculated at the CCSD(T)/cc-pVTZ + CP theory level. The hydrogen bond C–H···I was found to have an interaction energy of −0.5 kcal/mol. The I···I contact of type I (140°–140°) was found to be attractive with a well depth of −0.4 kcal/mol at a 4.6 Å distance, whereas type II contact (180°–90°) was found to be nearly twice more attractive. Its potential well depth reaches −0.7 kcal/mol at an I···I distance of 4.4 Å. These binding energies are therefore weaker than that of the typical hydrogen bonds. The AMOEBA force-field vdW parameters were fit to describe these interactions and used to predict the crystal structures. Our structure prediction, followed by density functional theorymany-body dispersion ranking established the noncentrosymmetric crystal packing to be the global minimum, in agreement with the experimental data. The coupled perturbed Kohn–Sham approach was used to estimate nonlinear susceptibility, and the predicted values were compared to that of the urea standard. The statistical analysis of the angular distribution for the I···I contacts in the predicted virtual polymorphs was compared to that found among the experimental crystal structures of iodoaromatic compounds. In both cases, symmetric (type I) contacts dominate for shorter and longer I···I distances, whereas L-shaped (type II) contacts are preferred for intermediate distances.

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“…There are several procedures described in the literature, , however they either make little use of molecular symmetry or use rather complicated algorithms. We have developed our own simple algorithm to convert atomic multipoles to multipole charge clusters (MCC) . In our approach, the monopole, dipole, and quadrupole can be represented as a set of 1 to 7 atomic charges (Figure ).…”

Section: Methodsmentioning

confidence: 99%

Quadrupole Correction: From Molecular Electrostatic Potential to Free Energies of Halogen Bonding

Titov

Shulga

Palyulin

2018

J. Chem. Theory Comput.

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Recently several molecular mechanics models of halogen bonding have been published. They describe the electrostatic potential anisotropy near the heavy halogen atom (known as a σ-hole) in different ways, ranging from an all-atom multipole expansion to a single positive extra-point charge. However, the question of a reasonable balance between the accuracy and the simplicity of the model remains open. In this work, we introduce the simplistic RESPQ electrostatics model built on the RESP charges complemented with fixed atomic quadrupoles. We show that it: (1) correctly describes the MEP anisotropy of aromatic halogen atoms, (2) improves the description of the halogen−water interaction energies in both halogen and hydrogen bonding cases, (3) provides an excellent estimation of solvation free energy differences of aromatic halogens, and (4) is compatible (with the help of multipole charge cluster approximation) with contemporary molecular modeling packages.

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Description of halogen bonding on the basis of multicenter multipole expansion

Cited by 10 publications

References 12 publications

Perspectives of Halogen Bonding Description in Scoring Functions and QSAR/QSPR: Substituent Effects in Aromatic Core

Perspectives of Halogen Bonding Description in Scoring Functions and QSAR/QSPR: Substituent Effects in Aromatic Core

First-Principles Crystal Engineering of Nonlinear Optical Materials. II. Effect of Halogen Bonds on the Structure and Properties of Triiodobenzenes

Quadrupole Correction: From Molecular Electrostatic Potential to Free Energies of Halogen Bonding

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