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Weatherly J, Macchi P, Volkov A. On the calculation of the electrostatic potential, electric field and electric field gradient from the aspherical pseudoatom model. II. Evaluation of the properties in an infinite crystal. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2021; 77:399-419. [PMID: 34473095 DOI: 10.1107/s2053273321005532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 05/28/2021] [Indexed: 11/10/2022]
Abstract
The previously reported exact potential and multipole moment (EP/MM) method for fast and precise evaluation of the intermolecular electrostatic interaction energies in molecular crystals using the pseudoatom representation of the electron density [Nguyen, Macchi & Volkov (2020), Acta Cryst. A76, 630-651] has been extended to the calculation of the electrostatic potential (ESP), electric field (EF) and electric field gradient (EFG) in an infinite crystal. The presented approach combines an efficient Ewald-type summation (ES) of atomic multipoles up to the hexadecapolar level in direct and reciprocal spaces with corrections for (i) the net polarization of the sample (the `surface term') due to a net dipole moment of the crystallographic unit cell (if present) and (ii) the short-range electron-density penetration effects. The rederived and reported closed-form expressions for all terms in the ES algorithm have been augmented by the expressions for the surface term available in the literature [Stenhammar, Trulsson & Linse (2011), J. Chem. Phys. 134, 224104] and the exact potential expressions reported in a previous study [Volkov, King, Coppens & Farrugia (2006), Acta Cryst. A62, 400-408]. The resulting algorithm, coded using Fortran in the XDPROP module of the software package XD, was tested on several small molecular crystal systems (formamide, benzene, L-dopa, paracetamol, amino acids etc.) and compared with a series of EP/MM-based direct-space summations (DS) performed within a certain number of unit cells generated along both the positive and negative crystallographic directions. The EP/MM-based ES technique allows for a noticeably more precise determination of the EF and EFG and significantly better precision of the evaluated ESP when compared with the DS calculations, even when the latter include contributions from an array of symmetry-equivalent atoms generated within four additional unit cells along each crystallographic direction. In terms of computational performance, the ES/EP/MM method is significantly faster than the DS calculations performed within the extended unit-cell limits but trails the DS calculations within the reduced summation ranges. Nonetheless, the described EP/MM-based ES algorithm is superior to the direct-space summations as it does not require the user to monitor continuously the convergence of the evaluated properties as a function of the summation limits and offers a better precision-performance balance.
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Affiliation(s)
- Jessie Weatherly
- Department of Chemistry and Computational Science Program, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Piero Macchi
- Department of Chemistry, Materials and Chemical Engineering, Politecnico di Milano, Via Mancinelli 7, Milano, 20131, Italy
| | - Anatoliy Volkov
- Department of Chemistry and Computational Science Program, Middle Tennessee State University, Murfreesboro, TN 37132, USA
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Nguyen D, Macchi P, Volkov A. 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 A-FOUNDATION AND ADVANCES 2020; 76:630-651. [PMID: 33125348 DOI: 10.1107/s2053273320009584] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 07/13/2020] [Indexed: 12/28/2022]
Abstract
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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Affiliation(s)
- Daniel Nguyen
- Department of Chemistry and Computational Science Program, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Piero Macchi
- Department of Chemistry, Materials and Chemical Engineering, Politecnico di Milano, Via Mancinelli 7, Milano 20131, Italy
| | - Anatoliy Volkov
- Department of Chemistry and Computational Science Program, Middle Tennessee State University, Murfreesboro, TN 37132, USA
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Nguyen D, Kisiel Z, Volkov A. Fast analytical evaluation of intermolecular electrostatic interaction energies using the pseudoatom representation of the electron density. I. The Löwdin α-function method. ACTA CRYSTALLOGRAPHICA A-FOUNDATION AND ADVANCES 2018; 74:524-536. [PMID: 30182939 DOI: 10.1107/s2053273318008690] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 06/13/2018] [Indexed: 11/11/2022]
Abstract
The previously reported [Volkov et al. (2004). Chem. Phys. Lett. 391, 170-175] exact potential and multipole moment (EP/MM) method for evaluation of intermolecular electrostatic interaction energies using the nuclei-centered pseudoatom representation of electron densities is significantly improved in terms of both speed and accuracy by replacing the numerical quadrature integration of the exact potential with a fully analytical technique. The resulting approach, incorporated in the XDPROP module of the software package XD, has been tested on several molecular systems ranging in size from water-water to dodecapeptide-dodecapeptide dimers using electron densities constructed via the University at Buffalo Aspherical Atom Databank. The improved hybrid method provides electrostatic interaction energies within the uncertainty of ≤0.2 kJ mol-1 for all benchmark systems. The running time for a dimer of a sizable, 225-atom dodecapeptide is under 4 s on a 2012 central processing unit (2.8 GHz AMD Opteron 6348) and under 3 s on a relatively modern processor (2.8 GHz Intel Xeon E3-1505M v5).
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Affiliation(s)
- Daniel Nguyen
- Department of Chemistry and Computational Science Program, Middle Tennessee State University, Murfreesboro, TN 37132, USA
| | - Zbigniew Kisiel
- Institute of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warszawa, Poland
| | - Anatoliy Volkov
- Department of Chemistry and Computational Science Program, Middle Tennessee State University, Murfreesboro, TN 37132, USA
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4
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Spackman MA. Towards the use of experimental electron densities to estimate reliable lattice energies. CrystEngComm 2018. [DOI: 10.1039/c8ce01108g] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Lattice energies derived from experimental charge densities are critically assessed, with a view to encouraging further research of this nature.
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Affiliation(s)
- Mark A. Spackman
- School of Molecular Sciences
- University of Western Australia
- Perth
- Australia
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5
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Turner MJ, Thomas SP, Shi MW, Jayatilaka D, Spackman MA. Energy frameworks: insights into interaction anisotropy and the mechanical properties of molecular crystals. Chem Commun (Camb) 2015; 51:3735-8. [PMID: 25525647 DOI: 10.1039/c4cc09074h] [Citation(s) in RCA: 355] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We present an approach to understanding crystal packing via 'energy frameworks', that combines efficient calculation of accurate intermolecular interaction energies with a novel graphical representation of their magnitude. In this manner intriguing questions, such as why some crystals bend with an applied force while others break, and why one polymorph of a drug exhibits exceptional tabletability compared to others, can be addressed in terms of the anisotropy of the topology of pairwise intermolecular interaction energies. This approach is applied to a sample of organic molecular crystals with known bending, shearing and brittle behaviour, to illustrate its use in rationalising their mechanical behaviour at a molecular level.
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Affiliation(s)
- Michael J Turner
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, WA, Australia.
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6
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Dittrich B, Matta CF. Contributions of charge-density research to medicinal chemistry. IUCRJ 2014; 1:457-69. [PMID: 25485126 PMCID: PMC4224464 DOI: 10.1107/s2052252514018867] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 08/20/2014] [Indexed: 06/04/2023]
Abstract
This article reviews efforts in accurate experimental charge-density studies with relevance to medicinal chemistry. Initially, classical charge-density studies that measure electron density distribution via least-squares refinement of aspherical-atom population parameters are summarized. Next, interaction density is discussed as an idealized situation resembling drug-receptor interactions. Scattering-factor databases play an increasing role in charge-density research, and they can be applied both to small-molecule and macromolecular structures in refinement and analysis; software development facilitates their use. Therefore combining both of these complementary branches of X-ray crystallography is recommended, and examples are given where such a combination already proved useful. On the side of the experiment, new pixel detectors are allowing rapid measurements, thereby enabling both high-throughput small-molecule studies and macromolecular structure determination to higher resolutions. Currently, the most ambitious studies compute intermolecular interaction energies of drug-receptor complexes, and it is recommended that future studies benefit from recent method developments. Selected new developments in theoretical charge-density studies are discussed with emphasis on its symbiotic relation to crystallography.
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Affiliation(s)
- Birger Dittrich
- Institut für Anorganische und Angewandte Chemie, Martin-Luther-King-Platz 6, 20146 Hamburg, Germany
| | - Chérif F. Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia B3M 2J6, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4J3M, Canada
- Department of Chemistry, Saint Mary’s University, Halifax, Nova Scotia B3H 3C3, Canada
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7
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Dittrich B, Hübschle CB, Pröpper K, Dietrich F, Stolper T, Holstein J. The generalized invariom database (GID). ACTA CRYSTALLOGRAPHICA SECTION B: STRUCTURAL SCIENCE 2013. [DOI: 10.1107/s0108768113002280] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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8
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Krawczuk A, Stadnicka K. Experimental and Theoretical Charge Density Study of the Chemical Bonding in Chlorokojic Acid Crystal Structure. J Phys Chem A 2012; 116:9759-68. [DOI: 10.1021/jp3058614] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anna Krawczuk
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow,
Poland
| | - Katarzyna Stadnicka
- Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow,
Poland
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9
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Mata I, Molins E, Amat M, Llor N, Checa B. C—H... X( X= O, N or π) interactions in benzyl carbamate. Acta Crystallogr C 2012; 68:o114-8. [DOI: 10.1107/s0108270112003186] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 01/25/2012] [Indexed: 11/11/2022] Open
Abstract
The crystal packing and interaction energy of benzyl carbamate, C8H9NO2, have been analysed in detail by thePIXELmethod. Benzyl carbamate forms layers of hydrogen-bonded molecules, with the layers connected by weaker C—H...π interactions. According to thePIXELanalysis, combinations of C—H...X(X= O, N or π) interactions are comparable in energy with hydrogen bonding. These interactions are necessary for explaining the geometry and the assembly of the layers.
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10
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Hathwar VR, Row TNG. Nature of Cl···Cl Intermolecular Interactions via Experimental and Theoretical Charge Density Analysis: Correlation of Polar Flattening Effects with Geometry. J Phys Chem A 2010; 114:13434-41. [DOI: 10.1021/jp1100413] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Venkatesha R. Hathwar
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012, India
| | - Tayur N. Guru Row
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore-560012, India
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11
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Chopra D, Guru Row TN, Arunan E, Klein RA. Crystalline ethane-1,2-diol does not have intra-molecular hydrogen bonding: Experimental and theoretical charge density studies. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2009.11.021] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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12
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Destro R, Soave R, Barzaghi M. Physicochemical properties of zwitterionic L- and DL-alanine crystals from their experimental and theoretical charge densities. J Phys Chem B 2008; 112:5163-74. [PMID: 18373373 DOI: 10.1021/jp710496q] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The total experimental electron density distributions rho(r) of zwitterionic L- and DL-alanine crystals, as derived from extensive sets of X-ray diffracted intensities collected at 23 and 19 K, are compared to gain an insight into the different physical properties of the two related chiral compounds in the solid state and to explore the extent of the rho(r) transferability. Relevant parameters that characterize the two crystal forms are obtained, showing differences and similarities in terms of (i) geometric descriptors, (ii) topological indexes, (iii) molecular electrostatic potential Phi(r) distributions, (iv) atomic volumes and charges, (v) molecular electric moments, and (vi) electrostatic interaction energies. To assess the relative stability of the racemate with respect to the pure enantiomer, the crystal lattice energies, as obtained through DFT fully periodic calculations, are also discussed and compared with the experimental sublimation enthalpies after correction for the proton-transfer energies. In-crystal group charges, evaluated with the quantum theory of atoms in molecules, are found to be transferable between the racemic and the pure enantiomer, at variance with group volumes. Similarly, molecular first and third moments are not strictly transferable and indicate that for the zwitterionic alanine molecule the molecular charge distribution in the DL-crystal is more polarized in the c direction by about 10%. By contrast, quantitative agreement is observed for second and fourth moments. Significant differences arise from (1) the crystal packing of the dipole vectors, which are aligned in an antiparallel fashion in the L-crystal, to be compared with a parallel alignment in the racemate, due the polar space group Pna21 of the latter, (2) the strongly attractive electrostatic energy of a homochiral pair in the L-crystal, which is opposed to the corresponding heterochiral pair in the DL-crystal form. The difference between these Ees values amounts to 135-150 kJ mol(-1). Despite this, the two crystal forms are predicted as equally thermodynamically favored by the theoretical P-B3LYP estimates of the crystal lattice energies. Finally, the necessity of an upgrading of the dispersion and exchange-repulsion terms currently adopted within the experimental charge density approach to intermolecular interactions is recognized and discussed.
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Affiliation(s)
- Riccardo Destro
- Dipartimento di Chimica Fisica ed Elettrochimica, Università di Milano, Via Golgi 19, 20133 Milano, Italy
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13
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Munshi P, Guru Row TN. Evaluation of weak intermolecular interactions in molecular crystalsviaexperimental and theoretical charge densities. CRYSTALLOGR REV 2005. [DOI: 10.1080/08893110500245899] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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14
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Volkov A, Coppens P. Calculation of electrostatic interaction energies in molecular dimers from atomic multipole moments obtained by different methods of electron density partitioning. J Comput Chem 2004; 25:921-34. [PMID: 15027105 DOI: 10.1002/jcc.20023] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Accurate and fast evaluation of electrostatic interactions in molecular systems is still one of the most challenging tasks in the rapidly advancing field of macromolecular chemistry, including molecular recognition, protein modeling and drug design. One of the most convenient and accurate approaches is based on a Buckingham-type approximation that uses the multipole moment expansion of molecular/atomic charge distributions. In the mid-1980s it was shown that the pseudoatom model commonly used in experimental X-ray charge density studies can be easily combined with the Buckingham-type approach for calculation of electrostatic interactions, plus atom-atom potentials for evaluation of the total interaction energies in molecular systems. While many such studies have been reported, little attention has been paid to the accuracy of evaluation of the purely electrostatic interactions as errors may be absorbed in the semiempirical atom-atom potentials that have to be used to account for exchange repulsion and dispersion forces. This study is aimed at the evaluation of the accuracy of the calculation of electrostatic interaction energies with the Buckingham approach. To eliminate experimental uncertainties, the atomic moments are based on theoretical single-molecule electron densities calculated at various levels of theory. The electrostatic interaction energies for a total of 11 dimers of alpha-glycine, N-acetylglycine and L-(+)-lactic acid structures calculated according to Buckingham with pseudoatom, stockholder and atoms-in-molecules moments are compared with those evaluated with the Morokuma-Ziegler energy decomposition scheme. For alpha-glycine a comparison with direct "pixel-by-pixel" integration method, recently developed Gavezzotti, is also made. It is found that the theoretical pseudoatom moments combined with the Buckingham model do predict the correct relative electrostatic interactions energies, although the absolute interaction energies are underestimated in some cases. The good agreement between electrostatic interaction energies computed with Morokuma-Ziegler partitioning, Gavezzotti's method, and the Buckingham approach with atoms-in-molecules moments demonstrates that reliable and accurate evaluation of electrostatic interactions in molecular systems of considerable complexity is now feasible.
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Affiliation(s)
- Anatoliy Volkov
- Department of Chemistry, State University of New York at Buffalo, 14260-3000, USA.
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Volkov A, Li X, Koritsanszky T, Coppens P. Ab Initio Quality Electrostatic Atomic and Molecular Properties Including Intermolecular Energies from a Transferable Theoretical Pseudoatom Databank. J Phys Chem A 2004. [DOI: 10.1021/jp0379796] [Citation(s) in RCA: 132] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anatoliy Volkov
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, and Department of Chemistry, Middle Tennessee State University, MTSU Box 0395, 1301 East Main Street, Murfreesboro, Tennessee 37132
| | - Xue Li
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, and Department of Chemistry, Middle Tennessee State University, MTSU Box 0395, 1301 East Main Street, Murfreesboro, Tennessee 37132
| | - Tibor Koritsanszky
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, and Department of Chemistry, Middle Tennessee State University, MTSU Box 0395, 1301 East Main Street, Murfreesboro, Tennessee 37132
| | - Philip Coppens
- Department of Chemistry, State University of New York at Buffalo, Buffalo, New York 14260-3000, and Department of Chemistry, Middle Tennessee State University, MTSU Box 0395, 1301 East Main Street, Murfreesboro, Tennessee 37132
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16
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Dittrich B, Scheins S, Paulmann C, Luger P. Transferability of Atomic Volumes and Charges in the Peptide Bond Region in the Solid State. J Phys Chem A 2003. [DOI: 10.1021/jp022584s] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Birger Dittrich
- Institut für Chemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany, and Mineralogisches Institut der Universität Hamburg, Grindelallee 48, D-20146 Hamburg, Germany
| | - Stephan Scheins
- Institut für Chemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany, and Mineralogisches Institut der Universität Hamburg, Grindelallee 48, D-20146 Hamburg, Germany
| | - Carsten Paulmann
- Institut für Chemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany, and Mineralogisches Institut der Universität Hamburg, Grindelallee 48, D-20146 Hamburg, Germany
| | - Peter Luger
- Institut für Chemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany, and Mineralogisches Institut der Universität Hamburg, Grindelallee 48, D-20146 Hamburg, Germany
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17
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Hibbs DE, Overgaard J, Gatti C, Hambley TW. The electron density in flavones I. Baicalein. NEW J CHEM 2003. [DOI: 10.1039/b301740k] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Li X, Wu G, Abramov YA, Volkov AV, Coppens P. Application of charge density methods to a protein model compound: calculation of Coulombic intermolecular interaction energies from the experimental charge density. Proc Natl Acad Sci U S A 2002; 99:12132-7. [PMID: 12221293 PMCID: PMC129410 DOI: 10.1073/pnas.192438999] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A combined experimental and theoretical charge density study of the pentapeptide Boc-Gln-d-Iva-Hyp-Ala-Phol (Boc, butoxycarbonyl; Gln, glutamine; Iva, isovaline; Hyp, hydroxyproline; Ala, ethylalanine; Phol, phenylalaninol) is described. The experimental analysis, based on synchrotron x-ray data collected at 20 K, is combined with ab initio theoretical calculations. The topologies of the experimental and theoretical densities are analyzed in terms of the atoms in molecules quantum theory. Topological parameters, including atomic charges and higher moments integrated over the atomic basins, have been evaluated with the program topxd and are used to calculate the electrostatic interactions between the molecules in the crystal. The interaction energies obtained after adding dispersive and repulsive van der Waals contributions agree quite well with those based on M-B3LYP/6-31G** dimer calculations for two of the three dimers in the crystal, whereas for the third a larger stabilization is obtained than predicted by the calculation. The agreement with theory is significantly better than that obtained with multipole moments derived directly from the aspherical atom refinement. The convergence of the interaction as a function of addition of successively higher moments up to and including hexadecapoles (l = 4) is found to be within 2-3 kJ/mol. Although shortcomings of both the theoretical and experimental procedures are pointed out, the agreement obtained supports the potential of the experimental method for the evaluation of interactions in larger biologically relevant molecules.
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Affiliation(s)
- Xue Li
- Chemistry Department, State University of New York, Buffalo, NY 14260-3000, USA
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19
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Gatti C, May E, Destro R, Cargnoni F. Fundamental Properties and Nature of CH··O Interactions in Crystals on the Basis of Experimental and Theoretical Charge Densities. The Case of 3,4-Bis(dimethylamino)-3-cyclobutene-1,2-dione (DMACB) Crystal. J Phys Chem A 2002. [DOI: 10.1021/jp013980y] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carlo Gatti
- CNR-ISTM, Istituto di Scienze e Tecnologie Molecolari, via C. Golgi 19, 20133 Milano, Italy, and Dipartimento di Chimica Fisica ed Elettrochimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Emanuela May
- CNR-ISTM, Istituto di Scienze e Tecnologie Molecolari, via C. Golgi 19, 20133 Milano, Italy, and Dipartimento di Chimica Fisica ed Elettrochimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Riccardo Destro
- CNR-ISTM, Istituto di Scienze e Tecnologie Molecolari, via C. Golgi 19, 20133 Milano, Italy, and Dipartimento di Chimica Fisica ed Elettrochimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
| | - Fausto Cargnoni
- CNR-ISTM, Istituto di Scienze e Tecnologie Molecolari, via C. Golgi 19, 20133 Milano, Italy, and Dipartimento di Chimica Fisica ed Elettrochimica, Università degli Studi di Milano, via C. Golgi 19, 20133 Milano, Italy
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20
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Affiliation(s)
- T S Koritsanszky
- Department of Chemistry, University of the Witwatersrand, WITS 2050, Johannesburg, South Africa
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