Ab Initio Charge Research Articles

Alloy informatics through ab initio charge density profiles: Case study of hydrogen effects in face-centred cubic crystals

Materials design has traditionally evolved through trial-error approaches, mainly due to the non-local relationship between microstructures and properties such as strength and toughness. We propose ‘alloy informatics’ as a machine learning based prototype predictive approach for alloys and compounds, using electron charge density profiles derived from first-principle calculations. We demonstrate this framework in the case of hydrogen interstitials in face-centred cubic crystals, showing that their differential electron charge density profiles capture crystal properties and defect-crystal interaction properties. Radial Distribution Functions (RDFs) of defect-induced differential charge density perturbations highlight the resulting screening effect, and, together with hydrogen Bader charges, strongly correlate to a large set of atomic properties of the metal species forming the bulk crystal. We observe the spontaneous emergence of classes of charge responses while coarse-graining over crystal compositions. Nudge-Elastic-Band calculations show that RDFs and charge features also connect to hydrogen migration energy barriers between interstitial sites. Unsupervised machine-learning on RDFs supports classification, unveiling compositional and configurational non-localities in the similarities of the perturbed densities. Electron charge density perturbations may be considered as bias-free descriptors for a large variety of defects.

Hydrogen Bonds of C=S, C=Se and C=Te with C-H in Small-Organic Molecule Compounds Derived from the Cambridge Structural Database (CSD)

Considerable interest in hydrogen bonding involving chalcogen has been growing since the IUPAC committee has redefined hydrogen bonding. Not only the focus is on unconventional acceptors, but also on donors not discussed before. It has been mentioned in previous studies that the proton of the H-C group could be involved in hydrogen bonding, but with conventional acceptors. In this study, we explored the ability of hydrogen bond formation of Se, S and Te acceptors with the H-C donor using Cambridge Structural Database in conjunction with Ab Initio calculations. In the CSD, there are respectively 256, 6249 and 11 R1,R2,-C=Se, R1,R2,-C=S and R1,R2,-C=Te structures that form hydrogen bonds, in which the N,N groups are majority. Except for C=S acceptor which can form a hydrogen bond with its C, C group, both C=Se and C=Te acceptors could form a hydrogen bond only with N,C and N,N groups. CSD analysis shows very similar d (norm) around -0.04 Å, while DFT-calculated interaction for N,C and N,N groups are also similar. Both interaction distances derived from CSD analysis and DFT-calculated interaction energies demonstrate that the acceptors form stable complexes with H-CF3. Besides hydrogen bonds, dispersion interactions are forces stabilizing the complexes since their contribution can reach 50%. Analysis of intra-molecular geometries and Ab Initio partial charges show that this bonding stems from resonance induced Cδ+=Xδ- dipoles. In many respects, both C=Se, C=S and C=Te are similar to C=S, with similar d (norm) and calculated interaction strengths.

Protein C-GeM: A Coarse-Grained Electron Model for Fast and Accurate Protein Electrostatics Prediction.

The electrostatic potential (ESP) is a powerful property for understanding and predicting electrostatic charge distributions that drive interactions between molecules. In this study, we compare various charge partitioning schemes including fitted charges, density-based quantum mechanical (QM) partitioning schemes, charge equilibration methods, and our recently introduced coarse-grained electron model, C-GeM, to describe the ESP for protein systems. When benchmarked against high quality density functional theory calculations of the ESP for tripeptides and the crambin protein, we find that the C-GeM model is of comparable accuracy to ab initio charge partitioning methods, but with orders of magnitude improvement in computational efficiency since it does not require either the electron density or the electrostatic potential as input.

Atom-based and Pharmacophore-based 3D - QSAR Studies on Vitamin D Receptor (VDR).

Vitamin D3 (1,25(OH)2D3) is a biologically active metabolite and plays a wide variety of regulatory functions in human systems. Currently, several Vitamin D analogues have been synthesized and tested against VDR (Vitamin D Receptor). Electrostatic potential methods are greatly influence the structure-based drug discovery. In this study, ab inito (DFT, HF, LMP2) and semi-empirical (RM1, AM1, PM3, MNDO, MNDO/d) charges were examined on the basis of their concert in predicting the docking pose using Induced Fit Docking (IFD) and binding free energy calculations against the VDR. Initially, we applied ab initio and semi-empirical charges to the 38 vitamin D analogues. Further, the charged analogues have been docked in the VDR active site. We generated the structure-based 3D-QSAR from the docked conformation of vitamin D analogues. On the other hand, we performed pharmacophore-based 3D-QSAR. The result shows that, AM1 is the good charge model for our study and AM1 charge based QSAR produced more accurate ligand poses. Furthermore, the hydroxyl group in the side chain of vitamin D analogues played an important role in the VDR antagonistic activity. Overall, we found that charge-based optimizations of ligands were out performed than the pharmacophore based QSAR model.

Multiple scattering approach to photoemission from the highest occupied molecular orbital of pentacene

Angle resolved photoemission spectroscopy (ARPES) gives detailed information about the surface electronic structures and oriented molecules. In the so-called orbital tomography method, the ARPES intensity is obtained by a simple Fourier transform of the initial state molecular orbital. While this method has given good results for a number of π-orbital systems, it is known to have strong limitations because the final state is approximated as a plane wave and thus photoelectron scattering is completely neglected. Here we propose an ARPES theory where the initial states are taken from a quantum chemistry method and the final states are calculated in multiple scattering theory. The initial molecular orbitals are reexpanded in a multi-site spherical wave basis and the multiple scattering potential is constructed from the ab initio charge density. These computations are performed algebraically using newly developed algorithms. The method is applied to pentance and the results are compared with the plane wave approximation.

High Efficiency and High Open Circuit Voltage in Quasi 2D Perovskite Based Solar Cells

An important property of hybrid layered perovskite is the possibility to reduce its dimensionality to provide wider band gap and better stability. In this work, 2D perovskite of the structure (PEA)2(MA)n–1PbnBr3n+1 has been sensitized, where PEA is phenyl ethyl‐ammonium, MA is methyl‐ammonium, and using only bromide as the halide. The number of the perovskite layers has been varied (n) from n = 1 through n = ∞. Optical and physical characterization verify the layered structure and the increase in the band gap. The photovoltaic performance shows higher open circuit voltage (Voc) for the quasi 2D perovskite (i.e., n = 40, 50, 60) compared to the 3D perovskite. Voc of 1.3 V without hole transport material (HTM) and Voc of 1.46 V using HTM have been demonstrated, with corresponding efficiency of 6.3% and 8.5%, among the highest reported. The lower mobility and transport in the quasi 2D perovskites have been proved effective to gain high Voc with high efficiency, further supported by ab initio calculations and charge extraction measurements. Bromide is the only halide used in these quasi 2D perovskites, as mixing halides have recently revealed instability of the perovskite structure. These quasi 2D materials are promising candidates for use in optoelectronic applications that simultaneously require high voltage and high efficiency.

First-principles simulation of light propagation and exciton dynamics in metal cluster nanostructures

We present a theoretical approach for the simulation of the electric field and exciton propagation in ordered arrays constructed of molecular-sized noble metal clusters bound to organic polymer templates. In order to describe the electronic coupling between individual constituents of the nanostructure we use the ab initio parameterized transition charge method which is more accurate than the usual dipole–dipole coupling. The electronic population dynamics in the nanostructure under an external laser pulse excitation is simulated by numerical integration of the time-dependent Schrodinger equation employing the fully coupled Hamiltonian. The solution of the TDSE gives rise to time-dependent partial point charges for each subunit of the nanostructure, and the spatio-temporal electric field distribution is evaluated by means of classical electrodynamics methods. The time-dependent partial charges are determined based on the stationary partial and transition charges obtained in the framework of the TDDFT. In order to treat large plasmonic nanostructures constructed of many constituents, the approximate self-consistent iterative approach presented in (Lisinetskaya and Mitric in Phys Rev B 89:035433, 2014) is modified to include the transition-charge-based interaction. The developed methods are used to study the optical response and exciton dynamics of $$\hbox{Ag}_{3}^{+}$$ and porphyrin-Ag4 dimers. Subsequently, the spatio-temporal electric field distribution in a ring constructed of ten porphyrin-Ag4 subunits under the action of circularly polarized laser pulse is simulated. The presented methodology provides a theoretical basis for the investigation of coupled light-exciton propagation in nanoarchitectures built from molecular size metal nanoclusters in which quantum confinement effects are important.

Can we treat ab initio atomic charges and bond orders as conformation-independent electronic structure descriptors?

It is shown that atomic charges and bond orders of 2′-deoxycytidine depend on the molecule conformation.

Robust molecular representations for modelling and design derived from atomic partial charges.

Ab initio derived atomic partial charges offer a simple, yet informative representation of the molecular electron density. We demonstrate the potential of different partial charge schemes for molecular descriptor construction. NPA and CM5 charges turned out to be largely conformation-independent and constitute representations of choice for molecular modelling and design.

Intriguing Electrostatic Potential of CO: Negative Bond-ends and Positive Bond-cylindrical-surface.

The strong electronegativity of O dictates that the ground state of singlet CO has positively charged C and negatively charged O, in agreement with ab initio charge analysis, but in disagreement with the dipole direction. Though this unusual phenomenon has been fairly studied, the study of electrostatic potential (EP) for noncovalent interactions of CO is essential for better understanding. Here we illustrate that both C and O atom-ends show negative EP (where the C end gives more negative EP), favoring positively charged species, whereas the cylindrical surface of the CO bond shows positive EP, favoring negatively charged ones. This is demonstrated from the interactions of CO with Na+, Cl–, H2O, CO and benzene. It can be explained by the quadrupole driven electrostatic nature of CO (like N2) with very weak dipole moment. The EP is properly described by the tripole model taking into account the electrostatic multipole moments, which has a large negative charge at a certain distance protruded from C, a large positive charge on C, and a small negative charge on O. We also discuss the EP of the first excited triplet CO.

How Does the Methodology of 3D Structure Preparation Influence the Quality of pKa Prediction?

The acid dissociation constant is an important molecular property, and it can be successfully predicted by Quantitative Structure-Property Relationship (QSPR) models, even for in silico designed molecules. We analyzed how the methodology of in silico 3D structure preparation influences the quality of QSPR models. Specifically, we evaluated and compared QSPR models based on six different 3D structure sources (DTP NCI, Pubchem, Balloon, Frog2, OpenBabel, and RDKit) combined with four different types of optimization. These analyses were performed for three classes of molecules (phenols, carboxylic acids, anilines), and the QSPR model descriptors were quantum mechanical (QM) and empirical partial atomic charges. Specifically, we developed 516 QSPR models and afterward systematically analyzed the influence of the 3D structure source and other factors on their quality. Our results confirmed that QSPR models based on partial atomic charges are able to predict pKa with high accuracy. We also confirmed that ab initio and semiempirical QM charges provide very accurate QSPR models and using empirical charges based on electronegativity equalization is also acceptable, as well as advantageous, because their calculation is very fast. On the other hand, Gasteiger-Marsili empirical charges are not applicable for pKa prediction. We later found that QSPR models for some classes of molecules (carboxylic acids) are less accurate. In this context, we compared the influence of different 3D structure sources. We found that an appropriate selection of 3D structure source and optimization method is essential for the successful QSPR modeling of pKa. Specifically, the 3D structures from the DTP NCI and Pubchem databases performed the best, as they provided very accurate QSPR models for all the tested molecular classes and charge calculation approaches, and they do not require optimization. Also, Frog2 performed very well. Other 3D structure sources can also be used but are not so robust, and an unfortunate combination of molecular class and charge calculation approach can produce weak QSPR models. Additionally, these 3D structures generally need optimization in order to produce good quality QSPR models.

Ab initio crystal structure and charge density distribution of a highly energetic 2,4-dinitrobenzoic acid molecule

The energetic parameters, such as density, bond strength, and sensitivity of explosives/ propellants decide their detonation power and safety. Experimentally, optimization of these parameters is found to be a difficult task; therefore, prior to synthesis, it makes sense to estimate these parameters by computational techniques, ab initio crystal structure prediction, and quantum chemical calculation coupled with the AIM analysis. Here, we predict the density of an energetic 2,4-dinitrobenzoic acid (DNBA) molecule from different ab initio crystal structure models and validate the results through comparisons with experimental data. The bond topological characterization reveals that the C NO2 bonds are the weakest bonds and are identified as sensitive bonds in the molecule. The bond sensitivity is estimated from Murray’s method. The impact sensitivity of this molecule is also calculated. Large negative electrostatic potential regions are found near the NO2 and carboxylic groups, which are the reactive sites of the molecule.

Relative Stability of Graphene Nanoflakes Under Environmentally Relevant Conditions

The stability of finite-sized graphene nanostructures under different conditions is contingent on the stability of the highly reactive undercoordinated atoms around the circumference. Chemical passivation is a convenient way of stabilizing the edges and corners, provided the conditions support adsorption. In this paper we examine the stabilities of hydrogen, oxygen, hydroxyl, and water functionalization of the edges of graphene nanoflakes using a combination of ab initio thermodynamics and self-consistent charge density functional tight-binding simulations. We find that the adsorption of hydrogen and oxygen on graphene nanoflakes is selective and sensitive to the edge and corner structure and the local environment. Under hydrogen-rich conditions (or in vacuo), we find that armchair edges are preferred, whereas under oxygen-rich conditions the stability of the zigzag edge is enhanced. In addition to this, we find that the types of corners play an important role, and the presence of acute 60° corners is thermodynamically preferred, particularly under humid conditions. In each case, the adsorption efficiency is related to the temperature and the pressure, which may be used to stabilize one type of structure or another.

ITP Adjuster 1.0: A New Utility Program to Adjust Charges in the Topology Files Generated by the PRODRG Server

The suitable computation of accurate atomic charges for the GROMACS topology *.itp files of small molecules, generated in the PRODRG server, has been a tricky task nowadays because it does not calculate atomic charges using an ab initio method. Usually additional steps of structure optimization and charges calculation, followed by a tedious manual replacement of atomic charges in the *.itp file, are needed. In order to assist this task, we report here the ITP Adjuster 1.0, a utility program developed to perform the replacement of the PRODRG charges in the *.itp files of small molecules by ab initio charges.

The effects of charge transfer on the aqueous solvation of ions

Ab initio-based charge partitioning of ionic systems results in ions with non-integer charges. This charge-transfer (CT) effect alters both short- and long-range interactions. Until recently, the effects of CT have been mostly neglected in molecular dynamics (MD) simulations. The method presented in this paper for including charge transfer between ions and water is consistent with ab initio charge partitioning and does not add significant time to the simulation. The ions of sodium, potassium, and chloride are parameterized to reproduce dimer properties and aqueous structures. The average charges of the ions from MD simulations (0.900, 0.919, and -0.775 for Na(+), K(+), and Cl(-), respectively) are consistent with quantum calculations. The hydration free energies calculated for these ions are in agreement with experimental estimates, which shows that the interactions are described accurately. The ions also have diffusion constants in good agreement with experiment. Inclusion of CT results in interesting properties for the waters in the first solvation shell of the ions. For all ions studied, the first shell waters acquire a partial negative charge, due to the difference between water-water and water-ion charge-transfer amounts. CT also reduces asymmetry in the solvation shell of the chloride anion, which could have important consequences for the behavior of chloride near the air-water interface.

HPAM: Hirshfeld partitioned atomic multipoles

An implementation of the Hirshfeld (HD) and Hirshfeld-Iterated (HD-I) atomic charge density partitioning schemes is described. Atomic charges and atomic multipoles are calculated from the HD and HD-I atomic charge densities for arbitrary atomic multipole rank l max on molecules of arbitrary shape and size. The HD and HD-I atomic charges/multipoles are tested by comparing molecular multipole moments and the electrostatic potential (ESP) surrounding a molecule with their reference ab initio values. In general, the HD-I atomic charges/multipoles are found to better reproduce ab initio electrostatic properties over HD atomic charges/multipoles. A systematic increase in precision for reproducing ab initio electrostatic properties is demonstrated by increasing the atomic multipole rank from l max = 0 (atomic charges) to l max = 4 (atomic hexadecapoles). Both HD and HD-I atomic multipoles up to rank l max are shown to exactly reproduce ab initio molecular multipole moments of rank L for L ⩽ l max . In addition, molecular dipole moments calculated by HD, HD-I, and ChelpG atomic charges only ( l max = 0 ) are compared with reference ab initio values. Significant errors in reproducing ab initio molecular dipole moments are found if only HD or HD-I atomic charges used. Program summary Program title: HPAM Catalogue identifier: AEKP_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEKP_v1_0.html Program obtainable from: CPC Program Library, Queenʼs University, Belfast, N. Ireland Licensing provisions: GNU General Public License v2 No. of lines in distributed program, including test data, etc.: 500 809 No. of bytes in distributed program, including test data, etc.: 13 424 494 Distribution format: tar.gz Programming language: C Computer: Any Operating system: Linux RAM: Typically, a few hundred megabytes Classification: 16.13 External routines: The program requires ‘formatted checkpoint’ files obtained from the Gaussian 03 or Gaussian 09 quantum chemistry program. Nature of problem: An ab initio molecular charge density ρ mol ( r ) is partitioned into Hirshfeld (HD) and Hirshfeld-Iterated (HD-I) atomic charge densities ρ a ( r ) on a grid. Atomic charges q a and multipoles Q l m a are calculated from the partitioned atomic charge densities ρ a ( r ) by numerical integration. Solution method: Molecular and isolated atomic grids are generated for the molecule of interest. The ab initio density matrix P μ ν and basis functions χ μ ( r ) are read in from ‘formatted checkpoint’ files obtained from the Gaussian 03 or 09 quantum chemistry programs. The ab initio density is evaluated for the molecule and the isolated atoms/atomic ions on grids and used to construct Hirshfeld (HD) and Hirshfeld-I (HD-I) partitioned atomic charges densities ρ a ( r ) , which are used to calculate atomic charges q a and atomic multipoles Q l m a by integration. Restrictions: The ab initio density matrix can be calculated at the HF, DFT, MP2, or CCSD levels with ab initio Gaussian basis sets that include up to s, p, d, f, g functions for either closed shell or open shell molecules. Running time: The running time varies with the size of the molecule, the size of the ab initio basis set, and the coarseness of the desired grid. The run time can range from a minute or less for water to ∼15 minutes for neopentane.

Nature and Stability of Weak Halogen Bonds in the Gas Phase: Molecular Beam Scattering Experiments and Ab Initio Charge Displacement Calculations

Molecular beam scattering experiments are presented for the first time in order to characterize the nature and strength of the intermolecular interaction of the gas phase H2O–CF4 and H2O–CCl4 weakl...

Ab initiocharge transfer multiplet calculations on theL2,3XANES and ELNES of3dtransition metal oxides

The ${L}_{2,3}$ x-ray absorption near-edge structures (XANES) and electron energy loss near-edge structures (ELNES) of $3d$ transition metal (TM) oxides are systematically calculated by the ab initio charge transfer multiplet (CTM) method using fully relativistic molecular spinors on the basis of density-functional theory. The electronic excitation from molecular spinors mainly composed of O-$2p$ to those of TM-$3d$, that is, charge transfer, is included by considering additional electronic configurations in the configuration interactions. The effects of the covalency and charge transfer on the TM-${L}_{2,3}$ XANES are investigated in detail. The power of the ab initio CTM method to quantitatively reproduce the spectra is demonstrated. Meanwhile, limitations of the application of the method are discussed.

Understanding the Surface Potential of Water

We have resolved the inconsistency in quantifying the surface potential at the liquid-vapor interface when using explicit ab initio electronic charge density and effective atomic partial charge models of liquid water. This is related, in part, to the fact that the resulting electric potentials from partial-charge models and ab initio charge distributions are quite different except for those regions of space between the molecules. We show that the electrostatic surface potential from a quantum mechanical charge distribution compares well to high-energy electron diffraction and electron holography measurements, as opposed to the comparison with electrochemical measurements. We suggest that certain regions of space be excluded when comparing computed surface potentials with electrochemical measurements. This work describes a novel interpretation of ab initio computed surface potentials through high-energy electron holography measurements as useful benchmarks toward a better understanding of electrochemistry.

Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field

The hydration free energy, structure, and dynamics of the zinc divalent cation are studied using a polarizable force field in molecular dynamics simulations. Parameters for the Zn(2+) are derived from gas-phase ab initio calculation of Zn(2+)-water dimer. The Thole-based dipole polarization is adjusted based on the Constrained Space Orbital Variations (CSOV) calculation while the Symmetry Adapted Perturbation Theory (SAPT) approach is also discussed. The vdW parameters of Zn(2+) have been obtained by comparing the AMOEBA Zn(2+)-water dimerization energy with results from several theory levels and basis sets over a range of distances. Molecular dynamics simulations of Zn(2+) solvation in bulk water are subsequently performed with the polarizable force field. The calculated first-shell water coordination number, water residence time and free energy of hydration are consistent with experimental and previous theoretical values. The study is supplemented with extensive Reduced Variational Space (RVS) and Electron Localization Function (ELF) computations in order to unravel the nature of the bonding in Zn(2+)(H(2)O)(n) (n=1,6) complexes and to analyze the charge transfer contribution to the complexes. Results show that the importance of charge transfer decreases as the size of Zn-water cluster grows due to anticooperativity and to changes in the nature of the metal-ligand bonds. Induction could be dominated by polarization when the system approaches condensed-phase and the covelant effects are eliminated from the Zn(II)-water interaction. To construct an "effective" classical polarizable potential for Zn(2+) in bulk water, one should therefore avoid over-fitting to the ab initio charge transfer energy of Zn(2+)-water dimer. Indeed, in order to avoid overestimation of condensed-phase many-body effects, which is crucial to the transferability of polarizable molecular dynamics, charge transfer should not be included within the classical polarization contribution and should preferably be either incorporated in to the pairwise van der Waals contribution or treated explicitly.