Verification of structural and electrostatic properties obtained by the use of different pseudoatom databases (original) (raw)
Related papers
Journal of Physical Chemistry A, 2004
The development of a theoretical databank of transferable pseudoatoms for fast prediction of the electron densities and related electronic properties of proteins is described. Chemically unique pseudoatoms identified on the basis of common connectivity and bonding are extracted from ab initio molecular densities of a large number of small molecules using a least-squares projection technique in Fourier transform space. The performance of the databank is evaluated by comparison of the electron densities and electrostatic properties of the amino acids GLN, SER, and LEU and their dimers with those obtained from molecular calculations on the same test compounds. It is found that deformation density bond peaks are reproduced to within 0.02-0.10 e/Å 3 , whereas electrostatic potentials, bond critical point indices, atomic charges, and molecular moments show differences with results from calculations performed directly on the test molecules which are comparable with or smaller than the spread of the values between different ab initio methods (Hamiltonian, basis set, etc.). The order of intermolecular electrostatic interaction energies for selected dimers of the test compounds are well reproduced, though the results are always smaller, by about 25 kJ/mol on average, than electrostatic energies from Morokuma-Ziegler decomposition of the total interaction energy evaluated with the ADF program. The difference is attributed to the limitations of the Buckingham-type approximation for electrostatic interactions, used in the current study, which assumes nonoverlapping charge densities. The consistency achieved by the pseudoatom databank is much better than that obtained with the AMBER99, CHARMM27, MM3, and MMFF94 force fields, which sometime overestimate, sometimes underestimate, the electrostatic interaction energy. The electrostatic component of the binding energies (directly related to the enthalpy of sublimation) of molecules in crystals, calculated based on the databank parameters, agree within 25-60 kJ/ mol with the total binding energies evaluated ab initio at the Density Functional level of theory, even though the exchange-repulsion and dispersion terms have not been taken into account in the databank values.
On the evaluation of molecular dipole moments from multipole refinement of X-ray diffraction data
Chemical Physics Letters, 1999
Lack of physical constraints in the purely mathematical multipole refinement model can lead to basis set oÕerlap errors in the evaluation of static molecular properties from X-ray diffraction data. For the molecular dipole moment, the error is large for several of the crystals tested in this study: DL-histidine, DL-proline, p-nitroaniline and p-amino-p X -nitrobiphenyl. Two restricted models are tested. In the first, atomic charges are constrained at k-refinement values, while in the second k X -values based on multipole refinements of theoretical ab-initio structure factors are used to reduce the flexibility of the model. Both models provide a more localized description of the pseudo atoms compared with an unrestricted refinement, but the k X -restricted model gives a more consistent representation of the molecular dipole moments and superior agreement with the theoretical deformation density for DL-histidine. q 1999 Elsevier Science B.V. All rights reserved.
CRYSTAL14: A program for theab initioinvestigation of crystalline solids
International Journal of Quantum Chemistry, 2014
The capabilities of the Crystal14 program are presented, and the improvements made with respect to the previous Crystal09 version discussed. Crystal14 is an ab initio code that uses a Gaussiantype basis set: both pseudopotential and all-electron strategies are permitted; the latter is not much more expensive than the former up to the first-second transition metal rows of the periodic table. A variety of density functionals is available, including as an extreme case Hartree-Fock; hybrids of various nature (global, range-separated, double) can be used. In particular, a very efficient implementation of global hybrids, such as popular B3LYP and PBE0 prescriptions, allows for such calculations to be performed at relatively low computational cost. The program can treat on the same grounds 0D (molecules), 1D (polymers), 2D (slabs), as well as 3D (crystals) systems. No spurious three-dimensional periodicity is required for low-dimensional systems as happens when plane-waves are used as a basis set. Symmetry is fully exploited at all steps of the calculation; this permits, for example, to investigate nanotubes of increasing radius at a nearly constant cost (better than linear scaling!) or to perform Self-Consistent-Field (SCF) calculations on fullerenes as large as (10,10), with 6000 atoms, 84000 atomic orbitals and 20 SCF cycles, on a single core in one day. Three versions of the code exist, serial, parallel and massive-parallel. In the second one the most relevant matrices are duplicated whereas in the third one the matrices in reciprocal space are distributed for diagonalization. All the relevant vectors are now dynamically allocated and deallocated after use, making Crystal14 much more agile than the previous version, in which they were statically allocated. The program now fits more easily in low-memory machines (as many supercomputers nowadays are). Crystal14 can be used on parallel machines up to a high number of cores (benchmarks up to 10240 cores are documented) with good scalability, the main limitation remaining the diagonalization step. Many tensorial properties can be evaluated in a fully automated way by using a single input keyword: elastic, piezoelectric, photoelastic, dielectric, as well as first and second hyperpolarizabilies, electric field gradients, Born tensors, etc. Many tools permit a complete analysis of the vibrational properties of crystalline compounds. The infrared and Raman intensities are now computed analytically and related spectra can be generated. Isotopic shifts are easily evaluated, frequencies of only a fragment of a large system computed and nuclear contribution to the dielectric tensor determined. New algorithms have been devised for the investigation of solid solutions and disordered systems. The topological analysis of the electron charge density, according to the Quantum Theory of Atoms in Molecules, is now incorporated in the code via the integrated merge of the Topond package. Electron correlation can be evaluated at the Möller-Plesset second order level (namely MP2) and a set of double-hybrids are presently available via the integrated merge with the Cryscor program.
Anisotropic atom-atom potentials based on X-ray molecular charge densities are applied in the evaluation of intermolecular interactions and lattice energies of crystals of glycylglycine, dl-histidine and dl-proline, p-nitroaniline and p-amino-p Hnitrobiphenyl. In parallel, calculations are performed on the molecular dimers (B3LYP) and on the periodic crystals with both Hartree-Fock (HF) and density functional theory (DFT) methods. The dimer interaction energies agree well with the Xray based values, except for the strongest interactions, which occur in the glycylglycine crystal and for p-amino-p H -nitrobiphenyl. The lack of agreement in these cases is attributed to the strong induced polarization of the molecular charge densities, which is not reproduced adequately by the dimer calculations.
Revised values for the X23 benchmark set of molecular crystals
Physical Chemistry Chemical Physics, 2019
We present revised reference values for cell volumes and lattice energies for the widely used X23 benchmark set of molecular crystals by including the effect of thermal expansion. For this purpose, thermally-expanded structures were calculated via the quasi-harmonic approximation utilizing three dispersion-inclusive density-functional approximations. Experimental unit-cell volumes were backcorrected for thermal and zero-point energy effects, allowing now a direct comparison with lattice relaxations based on electronic energies. For the derivation of reference lattice energies, we utilized harmonic vibrational contributions averaged over four density-functional approximations. In addition, the new reference values also take the change in electronic and vibrational energy due to thermal expansion into account. This is accomplished by either utilizing experimentally determined cell volumes and heat capacities, or by relying on the quasi-harmonic approximation. The new X23b reference values obtained this way will enable a more accurate benchmark for the performance of computational methods for molecular crystals.
C RYSTAL14 : A program for the ab initio investigation of crystalline solids
International Journal of Quantum Chemistry, 2014
The capabilities of the CRYSTAL14 program are presented, and the improvements made with respect to the previous CRYSTAL09 version discussed. CRYSTAL14 is an ab initio code that uses a Gaussiantype basis set: both pseudopotential and all-electron strategies are permitted; the latter is not much more expensive than the former up to the first-second transition metal rows of the periodic table. A variety of density functionals is available, including as an extreme case Hartree-Fock; hybrids of various nature (global, range-separated, double) can be used. In particular, a very efficient implementation of global hybrids, such as popular B3LYP and PBE0 prescriptions, allows for such calculations to be performed at relatively low computational cost. The program can treat on the same grounds zero-dimensional (molecules), one-dimensional (polymers), two-dimensional (slabs), as well as three-dimensional (3D; crystals) systems. No spurious 3D periodicity is required for low-dimensional systems as happens when plane-waves are used as a basis set. Symmetry is fully exploited at all steps of the calculation; this permits, for example, to investigate nanotubes of increasing radius at a nearly constant cost (better than linear scaling!) or to perform self-consistent-field (SCF) calculations on fullerenes as large as (10,10), with 6000 atoms, 84,000 atomic orbitals, and 20 SCF cycles, on a single core in one day. Three versions of the code exist, serial, parallel, and massive-parallel. In the second one, the most relevant matrices are duplicated, whereas in the third one the matrices in reciprocal space are distributed for diagonalization. All the relevant vectors are now dynamically allocated and deallocated after use, making CRYSTAL14 much more agile than the previous version, in which they were statically allocated. The program now fits more easily in low-memory machines (as many supercomputers nowadays are). CRYSTAL14 can be used on parallel machines up to a high number of cores (benchmarks up to 10,240 cores are documented) with good scalability, the main limitation remaining the diagonalization step. Many tensorial properties can be evaluated in a fully automated way by using a single input keyword: elastic, piezoelectric, photoelastic, dielectric, as well as first and second hyperpolarizabilies, electric field gradients, Born tensors and so forth. Many tools permit a complete analysis of the vibrational properties of crystalline compounds. The infrared and Raman intensities are now computed analytically and related spectra can be generated. Isotopic shifts are easily evaluated, frequencies of only a fragment of a large system computed and nuclear contribution to the dielectric tensor determined. New algorithms have been devised for the investigation of solid solutions and disordered systems. The topological analysis of the electron charge density, according to the Quantum Theory of Atoms in Molecules, is now incorporated in the code via the integrated merge of the TOPOND package. Electron correlation can be evaluated at the M€ oller-Plesset second-order level (namely MP2) and a set of double-hybrids are presently available via the integrated merge with the CRYSCOR program.
The Journal of Physical Chemistry B, 2000
We thank van Eijck and Kroon for pointing out some unintended ambiguities in our paper 1 and for giving us the opportunity to eliminate them. We hope that the following comments will clarify our position and how it diverges from that of van Eijck and Kroon. 2,3 This reply is organized as follows. In the first section, we describe the point of contention, namely, whether crystalstructure predictions should consider a correction to the electrostatic energy of polar crystals. (Consistent with normal usage, a polar crystal denotes a crystal whose unit cell has a nonzero dipole moment.) In the second section, we summarize and assess van Eijck and Kroon's arguments in favor of eliminating this correction a priori. In the third section, we describe our own protocol for crystal-structure prediction and consider briefly the three polymorphs of glycine mentioned by van Eijck and Kroon in their comment. In the final section, we address two other points raised by van Eijck and Kroon.