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Journal ArticleDOI

Evaluation of weak intermolecular interactions in molecular crystals via experimental and theoretical charge densities

01 Jul 2005-Crystallography Reviews (Taylor & Francis Group)-Vol. 11, Iss: 3, pp 199-241
TL;DR: In this article, Bader et al. presented an overview of the progress made in deriving one-electron properties, intermolecular interactions in terms of the Atoms in Molecule (AIM) approach (R.F.W.Bader, 1990), with special emphasis on improvements in charge density models and development of both experimental and theoretical techniques to interpret and analyse the nature of weak intermolescular interactions.
Abstract: Analysis of charge density distributions in molecular crystals has received considerable attention in the last decade both from high-resolution X-ray diffraction studies and from high-level theoretical calculations. An overview of the progress made in deriving one-electron properties, intermolecular interactions in terms of the Atoms in Molecule (AIM) approach (R.F.W. Bader. Atoms in Molecules-A Quantum Theory, Clarendon, Oxford (1990), R.F.W. Bader. J. Phys. Chem., A102, 7314 (1998)) is given with special emphasis on improvements in charge density models and development of both experimental and theoretical techniques to interpret and analyse the nature of weak intermolecular interactions. The significance of the derived results from the charge density of coumarin and its derivatives have been analysed to obtain insights into the nature of intermolecular C–H ··· O, C–H ··· π, π ··· π, C–H ··· S, and S ··· S contacts. The appearance of a ‘region of overlap’ to segregate hydrogen bonds from van der Waals in...

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Citations
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TL;DR: In this paper, the intrinsic strength of the DH and AH interactions is determined utilizing the properties of a well-defined set of local, uncoupled vibrational modes, and the local mode stretching force constant ka(HA) provides a unique measure of bond strength for both covalently and electrostatically bonded complexes.
Abstract: Local stretching modes for 69 different DH single bonds and 58 H···A H-bonds are calculated at the ωB97X-D/aug-cc-pVTZ level of theory to describe the changes in donor D and acceptor A upon forming the hydrogen-bonded complex. The intrinsic strength of the DH and AH interactions is determined utilizing the properties of a well-defined set of local, uncoupled vibrational modes. The local mode stretching force constant ka(HA) provides a unique measure of bond strength for both covalently and electrostatically bonded complexes. Generally applicable bond orders are derived, which can be related to the binding energies of the hydrogen bonded complexes. Although the red shifts in the DH stretching frequencies can be used to detect hydrogen bonding, they are not sufficient to assess the strength of hydrogen bonding. It is demonstrated that the calculated BSSE-corrected binding energies of hydrogen bonded complexes are related to the sum of bond order changes caused by hydrogen bonding. The covalent character of charge assisted hydrogen bonds is explained. Because local mode frequencies can also be derived from experimental normal mode frequencies, a new dimension in the study of hydrogen bonding is gained. © 2012 Wiley Periodicals, Inc.

118 citations

Journal ArticleDOI
TL;DR: The deformation electron densities, electrostatic potentials and interaction energies calculated for several tripeptides and aromatic molecules are calculated using ELMam2 electron-density parameters and compared with the former ELMAM database and density functional theory calculations.
Abstract: ELMAM2 is a generalized and improved library of experimentally derived multipolar atom types. The previously published ELMAM database is restricted mostly to protein atoms. The current database is extended to common functional groups encountered in organic molecules and is based on optimized local axes systems taking into account the local pseudosymmetry of the molecular fragment. In this approach, the symmetry-restricted multipoles have zero populations, while others take generally significant values. The various applications of the database are described. The deformation electron densities, electrostatic potentials and interaction energies calculated for several tripeptides and aromatic molecules are calculated using ELMAM2 electron-density parameters and compared with the former ELMAM database and density functional theory calculations.

100 citations

Journal ArticleDOI
TL;DR: The local hydrogen bond (HB) stretching frequencies are at 676 cm−1 and by this 482 and 412 cm −1 higher compared to the measured symmetric and asymmetric HB stretching frequencies at 264 and 194 cm− 1 as mentioned in this paper.
Abstract: The 24 normal and 24 local vibrational modes of the formic acid dimer formed by two trans formic acid monomers to a ring (TT1) are analysed utilising preferentially experimental frequencies, but also CCSD(T)/CBS and ωB97X-D harmonic vibrational frequencies. The local hydrogen bond (HB) stretching frequencies are at 676 cm−1 and by this 482 and 412 cm−1 higher compared to the measured symmetric and asymmetric HB stretching frequencies at 264 and 194 cm−1. The adiabatic connection scheme between local and normal vibrational modes reveals that the lowering is due to the topology of dimer TT1, mass coupling, and avoided crossings involving the H⋅⋅⋅OC bending modes. The HB local mode stretching force constant is related to the strength of the HB whereas the normal mode stretching force constant and frequency lead to an erroneous underestimation of the HB strength. The HB in TT1 is stabilised by electron delocalisation in the O=C–O units fostered by forming a ring via double HBs. This implies that the CO apart ...

75 citations

Journal ArticleDOI
TL;DR: An improved methodology is presented, incorporating information on internal vibrational motion from ab initio cluster calculations using the ONIOM approach implemented in GAUSSIAN03, and offers considerable promise in future charge-density studies of molecular crystals.
Abstract: X-ray diffraction data cannot provide anisotropic displacement parameters (ADPs) for H atoms, a major outstanding problem in charge-density analysis of molecular crystals. Although neutron diffraction experiments are the preferred source of this information, for a variety of reasons they are possible only for a minority of materials of interest. To date, approximate procedures combine rigid-body analysis of the molecular heavy-atom skeleton, based on ADPs derived from the X-ray data, with estimates of internal motion provided by spectroscopic data, analyses of neutron diffraction data on related compounds, or ab initio calculations on isolated molecules. Building on these efforts, an improved methodology is presented, incorporating information on internal vibrational motion from ab initio cluster calculations using the ONIOM approach implemented in GAUSSIAN03. The method is tested by comparing model H-atom ADPs with reference values, largely from neutron diffraction experiments, for a variety of molecular crystals: benzene, 1-methyluracil, α-glycine, xylitol and 2-methyl-4-nitroaniline. The results are impressive and, as the method is based on widely available software, and is in principle widely applicable, it offers considerable promise in future charge-density studies of molecular crystals.

60 citations

Journal ArticleDOI
TL;DR: This quantitative and comparative study shows that in the absence of high-resolution diffraction data, the database transfer approach can be applied to the multipolar electron density features very accurately.
Abstract: The multipolar atom model, constructed by transferring the charge-density parameters from an experimental or theoretical database, is considered to be an easy replacement of the widely used independent atom model. The present study on a new crystal structure of quercetin monohydrate [2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-4H-chromen-4-one monohydrate], a plant flavonoid, determined by X-ray diffraction, demonstrates that the transferred multipolar atom model approach greatly improves several factors: the accuracy of atomic positions and the magnitudes of atomic displacement parameters, the residual electron densities and the crystallographic figures of merit. The charge-density features, topological analysis and electrostatic interaction energies obtained from the multipole models based on experimental database transfer and periodic quantum mechanical calculations are found to compare well. This quantitative and comparative study shows that in the absence of high-resolution diffraction data, the database transfer approach can be applied to the multipolar electron density features very accurately.

59 citations

References
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Journal ArticleDOI
TL;DR: In this article, a semi-empirical exchange correlation functional with local spin density, gradient, and exact exchange terms was proposed. But this functional performed significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol.
Abstract: Despite the remarkable thermochemical accuracy of Kohn–Sham density‐functional theories with gradient corrections for exchange‐correlation [see, for example, A. D. Becke, J. Chem. Phys. 96, 2155 (1992)], we believe that further improvements are unlikely unless exact‐exchange information is considered. Arguments to support this view are presented, and a semiempirical exchange‐correlation functional containing local‐spin‐density, gradient, and exact‐exchange terms is tested on 56 atomization energies, 42 ionization potentials, 8 proton affinities, and 10 total atomic energies of first‐ and second‐row systems. This functional performs significantly better than previous functionals with gradient corrections only, and fits experimental atomization energies with an impressively small average absolute deviation of 2.4 kcal/mol.

87,732 citations

Journal ArticleDOI
TL;DR: Numerical calculations on a number of atoms, positive ions, and molecules, of both open- and closed-shell type, show that density-functional formulas for the correlation energy and correlation potential give correlation energies within a few percent.
Abstract: A correlation-energy formula due to Colle and Salvetti [Theor. Chim. Acta 37, 329 (1975)], in which the correlation energy density is expressed in terms of the electron density and a Laplacian of the second-order Hartree-Fock density matrix, is restated as a formula involving the density and local kinetic-energy density. On insertion of gradient expansions for the local kinetic-energy density, density-functional formulas for the correlation energy and correlation potential are then obtained. Through numerical calculations on a number of atoms, positive ions, and molecules, of both open- and closed-shell type, it is demonstrated that these formulas, like the original Colle-Salvetti formulas, give correlation energies within a few percent.

84,646 citations

Journal ArticleDOI
TL;DR: In this paper, a direct difference method for the computation of molecular interactions has been based on a bivariational transcorrelated treatment, together with special methods for the balancing of other errors.
Abstract: A new direct difference method for the computation of molecular interactions has been based on a bivariational transcorrelated treatment, together with special methods for the balancing of other errors. It appears that these new features can give a strong reduction in the error of the interaction energy, and they seem to be particularly suitable for computations in the important region near the minimum energy. It has been generally accepted that this problem is dominated by unresolved difficulties and the relation of the new methods to these apparent difficulties is analysed here.

19,483 citations

Journal ArticleDOI
TL;DR: L Lists of software presented and~or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availability of the software where this is known.
Abstract: Computer Program Abstracts The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and significant updates to existing ones. Following normal submission, a Computer Program Abstract will be reviewed by one or two members of the IUCr Commission on Crystallographic Computing. It should not exceed 500 words in length and should follow the standard format given on page 189 of the June 1985 issue of the Journal [J. Appl. CrysL (1985). 18, 189190] and on the World Wide Web at http://www.iucr. ac. uk/journals/jac/software/. Lists of software presented and~or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availability of the software where this is known. J. App/. CrysL (1997). 30, 565 ORTEP-3 for Windows a version of ORTEP-III with a Graphical User Interface (GUI)

19,468 citations

Journal ArticleDOI
TL;DR: The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and signi®cant updates to existing ones.
Abstract: The category Computer Program Abstracts provides a rapid means of communicating up-to-date information concerning both new programs or systems and signi®cant updates to existing ones. Following normal submission, a Computer Program Abstract will be reviewed by one or two members of the IUCr Commission on Crystallographic Computing. It should not exceed 500 words in length and should follow the standard format given on page 189 of the June 1985 issue of the Journal [J. Appl. Cryst. (1985). 18, 189± 190] and on the World Wide Web at http://www.iucr. org/journals/jac/software/. Lists of software presented and/or reviewed in the Journal of Applied Crystallography are available on the World Wide Web at the above address, together with information about the availability of the software where this is known.

18,151 citations