Properties Of Atoms In Molecules Research Articles

Thermal decomposition mechanisms of some amino acid ionic liquids: Molecular approach

In this study, the thermal decomposition mechanism of the amino acid ionic liquids (AAILs) including 1-ethyl-3-methylimidazolium ([Emim]) as the cation and Glycinate, Alaninate, Valinate, and Leucinate as the anions was investigated from the molecular approach. Different mechanisms of SN2, Hofmann elimination and alkyl rearrangement were proposed. These mechanisms were analyzed based on the steric hindrance effect of the alky groups and the nucleophilicity of the carboxylate and amine groups of the amino acid anions. SN2 and alkyl rearrangement mechanisms are the preferred routes of the reaction from the kinetic and thermodynamic viewpoints. Among all AAILs, [Emim][Ala] has the lowest thermal stability. To have an insight into the stability of the AAILs, topological properties and quantum chemistry reactivity indices (QCRI) were investigated and discussed. On the basis of QCRI analysis, low stability of [Emim][Ala] can be related to the lower electronic chemical hardness and greater positive character of the electrophilicity index in comparison with other AAILs. Moreover, the nature and energy of interactions at the transition states of decomposition reactions were evaluated by using the natural bond orbital method and atoms in molecules properties.

Relativistic (SR-ZORA) quantum theory of atoms in molecules properties.

The Quantum Theory of Atoms in Molecules (QTAIM) is used to elucidate the effects of relativity on chemical systems. To do this, molecules are studied using density-functional theory at both the nonrelativistic level and using the scalar relativistic zeroth-order regular approximation. Relativistic effects on the QTAIM properties and topology of the electron density can be significant for chemical systems with heavy atoms. It is important, therefore, to use the appropriate relativistic treatment of QTAIM (Anderson and Ayers, J. Phys. Chem. 2009, 115, 13001) when treating systems with heavy atoms. © 2016 Wiley Periodicals, Inc.

Machine Learning for Quantum Mechanical Properties of Atoms in Molecules

We introduce machine learning models of quantum mechanical observables of atoms in molecules. Instant out-of-sample predictions for proton and carbon nuclear chemical shifts, atomic core level excitations, and forces on atoms reach accuracies on par with density functional theory reference. Locality is exploited within non-linear regression via local atom-centered coordinate systems. The approach is validated on a diverse set of 9k small organic molecules. Linear scaling of computational cost in system size is demonstrated for saturated polymers with up to sub-mesoscale lengths.

Stilbene photoisomerization driving force as revealed by the topology of the electron density and QTAIM properties

The photoisomerization of stilbene (C14H12) has become an archetype for the study of cis-trans isomerizations induced by light. Despite the many electronic structure calculations performed to gain understanding about this important process, no insight about this reaction has been obtained by means of the exploitation of topological quantum chemical methods. This contribution addresses the changes of the topology of the electron density along with those of the properties of atoms in molecules undergone throughout this photochemical transformation. By considering the phenyl rings and the CHCH bridge of stilbene separately, we found that both groups in the ground state are destabilized when the system evolves from either the cis or trans isomer towards the conical intersection connecting the S0 and S1 states. Nonetheless, the energy of the C6H5 moieties across the excited state potential energy curve is reduced along the same change in configuration of C14H12, thereby providing the driving force for the reaction to occur. The analysis of the atomic charges reveals that the carbon atoms of the CHCH bridge withdraw electron density from their interatomic region between them and the phenyl groups. This flow of charge density might be related with the occupation of the CHCH π★ orbital which allows the reaction to take place. Finally, an examination of the electronegativity of the groups CHCH and C6H5 indicates that the phenyl rings drastically change their electronegative nature upon photoexcitation, enabling the system to undergo the photoisomerization. Overall, it is shown how the topological analysis of the electron density can provide important insights about chemical reactions carried out in excited states.

Toward the multi-component quantum theory of atoms in molecules: a variational derivation

The general formalism of an extended quantum theory of atoms in molecules (QTAIM) dealing with the multi-component quantum systems, composed of various types of quantum particles, is disclosed in this contribution. This novel methodology, termed as the multi-component QTAIM (MC-QTAIM), is able to deal with non-adiabatic ab initio wavefunctions extracting atoms in molecules quantifying their properties. It can also be applied to elucidate the AIM structure of exotic species and bound quantum systems consisting of fundamental elementary particles like positrons and muons. The formalism is based on the previously disclosed density combination idea that is extended to derive the multi-component subsystem hypervirial theorem as well as the extended subsystem energy functional. Through the extended subsystem variational procedure, inspired from Schrodinger’s original variational principle, the surface terms containing the flux of the current property densities are derived. Accordingly, the extended Gamma field is introduced during this variational procedure that is used as the basic scalar field in the topological analysis yielding atoms in molecules and their real space boundaries. The Gamma field is central to the MC-QTAIM, replacing the usual one-electron density employed in the orthodox QTAIM and corresponding topological analysis. Through the multi-component hypervirial theorem, various regional theorems are derived which are then used to quantify the mechanical properties of atoms in molecules; these include the force, virial, torque, power, continuity and current theorems. In order to demonstrate the capability of the formalism, isotopically asymmetric hydrogen molecules, HD, HT and DT as well as YX systems (Y = 6Li, 7Li; X = H, D, T) composed of electrons and two different nuclei, all treated equally as quantum waves instead of clamped particles, are analyzed within context of the MC-QTAIM. The resulting computational analysis demonstrates that the MC-QTAIM is able to yield reasonable topological structures similar to those observed previously for diatomic species within context of the orthodox QTAIM. The asymmetrical nature of these species, inherent in their non-Born–Oppenhiemer wavefunctions, manifests itself clearly in the MC-QTAIM analysis yielding two distinguishable atomic basins with different properties. These differences are rationalized generally by the observed electron transfer from one basin to the other. Finally, some possible future theoretical extensions are considered briefly.

The two-component quantum theory of atoms in molecules (TC-QTAIM): foundations

The foundations of the two-component quantum theory of atoms in molecules (TC-QTAIM) are addressed in this contribution. In this regard, the theory is presented in an axiomatic manner and the main theorems describing regional properties of atoms in molecules are considered in detail. This is an extension of the orthodox quantum theory of atoms in molecules (QTAIM) for dealing with non-adiabatic wavefunctions of usual molecules as well as extracting the regional quantum structure of exotic species from the corresponding wavefunctions. The best examples of the latter are positronic and muonic species. The computational study of a model system consisting of a clamped lithium nucleus, four electrons, and a positively charged quantum particle carrying a unit of positive charge with a variable mass, m = 200–1013 me, supplements the theoretical argument demonstrating unambiguously that the TC-QTAIM analysis yields reasonable results. It reveals that the contribution of the positively charged particle in the topological analysis and basin properties is non-negligible. Most importantly, it is demonstrated that by increasing the mass of the positive particle, the TC-QTAIM analysis tends toward the QTAIM analysis of the lithium hydride system considered within the clamped nucleus paradigm. This result seems to indicate that the orthodox QTAIM is just the asymptote of the TC-QTAIM, the latter encompasses the former. Thus, one may claim that the TC-QTAIM is a unified framework for the AIM analysis of vast variety of quantum systems.

The influence of density functional approximations on the description of LiH + NH 3 → LiNH 2 + H 2 reaction

In this Letter, we assess the ability of various density functionals to correctly describe the pathway of the simple reaction LiH + NH 3 → LiNH 2 + H 2, a model for hydrogen storage in recent lithium-based materials. To this aim, the ability of 27 exchange–correlation approximations for providing accurate reaction energies, activation barriers and local Bader’s Atoms in Molecules properties is evaluated. Lastly, conceptual DFT is used to broaden the scope of possible relevant interpretative tools.

First-principle study of interaction of H2 and H2O molecules with (ZnO)n(n=3–6) ring clusters

AbstractA density functional calculation was performed to investigate the impact of hydrogen and water molecules on zinc oxide clusters (ZnO)n=3–6… X, where X=H2 and H2O. The calculated binding energies were corrected for the basis set superposition error (BSSE). The structural parameters and chemical hardness were calculated for the complexes of zinc oxide clusters and guest molecules. The strength values of the interaction between the clusters and the guest molecules were analyzed based on the topological properties of atoms in molecules (AIM) theory of Bader. The stereo electronic interactions inside the ZnO clusters were analyzed in detail using the natural bond orbital (NBO) analysis.

Molecular interaction of H 2 and H 2O molecules with the boron nitride (BN) n=3–5 clusters: A theoretical study

A density functional theory study and single point energy calculation at MP2/6-311++G** level of theory have been performed to know the impact of hydrogen and water molecules on boron nitride clusters (BN) n=3–5 ⋯X, where X=H 2 and H 2O. The calculated binding energies have been corrected for the basis set superposition error (BSSE). The change in structural parameters, molecular volume, and chemical hardness values were calculated for the boron nitride clusters when the guest molecules interact with the cluster. The strength of the weak interaction between the clusters and the guest molecules were analyzed using the topological properties of Atoms in Molecules (AIM) theory of Bader. The factors which influence the strength of the interaction between the clusters and the guest molecules are due to the stereo electronic interactions inside the BN clusters, these have been analyzed in detail using the Natural Bond Orbital (NBO) analysis.

Properties of Atoms in Molecules: Caged Atoms and the Ehrenfest Force

This paper uses the properties of atom X enclosed within an adamantane cage, denoted by X@C10H16, as a vehicle to introduce the Ehrenfest force into the discussion of bonding, the properties being determined by the physics of an open system. This is the force acting on an atom in a molecule and determining the potential energy appearing in Slater's molecular virial theorem. The Ehrenfest force acting across the interatomic surface of a bonded pair atoms [Formula: see text] atoms linked by a bond path [Formula: see text] is attractive, each atom being drawn toward the other, and the associated surface virial that measures the contribution to the energy arising from the formation of the surface is stabilizing. It is the Ehrenfest force that determines the adhesive properties of surfaces. The endothermicity of formation for X = He or Ne is not a result of instabilities incurred in the interaction of X with the four methine carbons to which it is bonded, interactions that are stabilizing both in terms of the changes in the atomic energies and in the surface virials. The exothermicity for X = Be(2+), B(3+), and Al(3+) is a consequence of the transfer of electron density from the hydrogen atoms to the carbon and X atoms, the exothermicity increasing with charge transfer despite an increase in the contained volume of X.

Molecular Design of Bis-Chelate N-Donor-Stabilized Silaethenes: Theoretical Study of 1,1-Bis[N-(dimethylamino)acetimidato]silene

RHF/6-31G* and B3LYP/6-31G* computations were performed on the silene [Me2NNC(Me)O]2SiCH2 (6) and analyzed through the use of properties of atoms in molecules. Three stationary states of 6 belong to its non-chelate (6a) and two intramolecularly N-donor-stabilized forms, five-membered mono-chelate (6b) and previously unknown (for the silenes) bis-chelate (6c), with three-, four-, and five-coordinate doubly bonded silicon, respectively. On going from 6a to 6b and 6c, initially planar silicon attains distorted tetrahedral and square pyramidal structures, whereas the SiC double bond becomes more polar and changes its distance from 1.674 Å to 1.693 and 1.704 Å and from 1.691 Å to 1.701 and 1.713 Å at the RHF and B3LYP levels, respectively. The RHF and B3LYP N−Si distances in 6b (1.988 and 2.031 Å) are shorter than in 6c (2.187 and 2.140 Å). The N→Si bond in chelates 6b,c is described as highly polar, but of sufficiently covalent character. The four-center six-electron (4c-6e) model is proposed for the silicon bonding in the N2SiC moiety of 6c. High energetic advantages of the chelate 6b and 6c forms over 6a (26.8 and 31.4 kcal/mol at the B3LYP/6-31G* level including the ZPE correction and 32.4 and 36.3 kcal/mol at the RHF/6-31G* level, respectively) suggest that intramolecular N-donor stabilization may be sufficient to observe silene 6 under relatively mild conditions.

Hydrogen bonding, solvation, and hydrolysis of cisplatin: a theoretical study.

Density functional calculations on a range of hydrogen bonded clusters of cisplatin are reported. A systematic search of 1:1 cisplatin:water complexes reveals only three stable minima, which contain a number of common, recurring interactions, such as an N-H...O-H...Cl bridging mode. Expanding these clusters by adding water molecules leads to a model of the first solvation shell of cisplatin, which contains the above motifs along with several strong water-water interactions. The strengths of such interactions are rationalized on the basis of electrostatic potentials, and quantified by use of Atoms in Molecules properties. This analysis also allows us to estimate cisplatin's position on Abraham's hydrogen bond acidity and basicity scales, indicating that cisplatin is a strong donor and acceptor of hydrogen bonds due to the dominance of hard, electrostatic interactions. The effects of this explicit solvation on the barrier to hydrolysis, and hence activation, of cisplatin are explored, indicating a slightly higher barrier than in the gas phase, leading to better agreement with experiment than either gas phase or continuum solvation calculations.

Complementary nature of hydrogen bond basicity and acidity scales from electrostatic and atoms in molecules properties

DFT calculations over 120 hydrogen bond bases/acids and their complexes with hydrogen fluoride/hydrogen cyanide have been performed. By using properties computed at the B3LYP/6-31+G(d,p) level of theory as predictors of ∑βH2/∑αH2 in multivariate analysis, the overall hydrogen bond scale can be regarded as a composite descriptor made of an electrostatic term (by using minimum/maximum electrostatic potential values on the 0.001 au isodensity contour surface of the isolated base/acid) and of an overlap term (by using energy density values calculated at the bond critical point of 1∶1 HF/NCH complexes). These models underline the complementarity between the two overall hydrogen bond scales, and, for the first time, make accurate predictions for multi-functional bases/acids.

Update of the AIM2000-program for atoms in molecules.

The second version of the program package AIM2000 is presented. AIM2000 makes use of the well established theory of atoms in molecules. AIM2000 analyzes the molecular structure and calculates properties of atoms in molecules as well as properties of interatomic surfaces. The program has an interactive, context-sensitive help component and extensive 2D and 3D visualization components.

Properties of atoms in molecules: Construction of one-density matrix from functional group densities

The demonstrated transferability of functional groups defined as proper open systems within the theory of atoms in molecules is used to iteratively construct a one-electron density matrix P and its derived electron density distribution. The initial guess at the density used in the fitting procedure is obtained from the addition of the density distributions of groups defined in parent molecules by the maximal matching of their interatomic surfaces. The method thus takes advantage of the observation that the “zero-flux” boundary condition defining a proper open system maximizes the transferability of the density distribution of a given group between molecules, one that is accompanied by a paralleling transferability in all of its properties. The construction is subject to the constraints that P be idempotent and normalized. The method is applied to the construction of P for the molecules HCH2|CH2X, with X=CH3, NH2, OH, and F, where the vertical bar denotes the new C–C interatomic surface, the new zero-flux boundary. The densities for the groups HCH2| and |CH2X are defined in their dimer molecules, HCH2|CH2H and XCH2|CH2X.

Properties of atoms in molecules: Transition probabilities

The transition probability for electric dipole transitions is a measurable property of a system and is therefore, partitionable into atomic contributions using the physics of a proper open system. The derivation of the dressed property density, whose averaging over an atomic basin yields the atomic contribution to a given oscillator strength, is achieved through the development of perturbation theory for an open system. A dressed density describes the local contribution resulting from the interaction of a single electron at some position r, as determined by the relevant observable, averaged over the motions of all of the remaining particles in the system. In the present work, the transition probability density expressed in terms of the relevant transition density, yields a local measure of the associated oscillator strength resulting from the interaction of the entire molecule with a radiation field. The definition of the atomic contributions to the oscillator strength enables one to determine the extent to which a given electronic or vibrational transition is spatially localized to a given atom or functional group. The concepts introduced in this article are applied to the Rydberg-type transitions observed in the electronic excitation of a nonbonding electron in formaldehyde and ammonia. The atomic partitioning of the molecular density distribution and of the molecular properties by surfaces of zero flux in the gradient vector field of the electron density, the boundary condition defining the physics of a proper open system, is found to apply to the density distributions of the excited, Rydberg states.

Properties of Atoms in Molecules: Group Additivity

Every property of a molecule is given by the sum of the contributions from each of its constituent atoms or groups, the groups being defined as proper open systems. The observation of “experimental group additivty” requires that in addition to the properties of the groups being additive, the group and its properties be transferable from one molecule to another, different molecule. It is shown that such transferability of a group and its properties is in general, only apparent, being the result of compensatory transferability wherein the changes in the properties of one group are compensated for by equal but opposite changes in the properties of the adjoining group. These compensating changes are in some cases vanishingly small, but even when the energy changes are in excess of 20 kcal/mol, the experimental heat of formation is still predicted to be additive to within 0.1 kcal/mol. The operation of compensatory transferability is illustrated for the linear homologous series of hydrocarbons and polysilanes ...

Calculation of atomic integration data

The calculation of average properties of atoms in molecules and interatomic surfaces is a difficult problem that requires the evaluation of two- and three-dimensional integrals over regions with nontrivial borders. A mathematical formalism is presented that maps these regions onto the whole of ℝ2 and/or ℝ3 and allows the construction of efficient and reliable numerical methods for the calculation of these integrals. These methods, which will be part of a forthcoming program package, are described and examples are given. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1040–1048, 2000

Properties of atoms in molecules: Atoms under pressure

The in situ pressure acting on the surface of an open system at the atomic level is defined and determined by the virial theorem for a proper open system, one whose spatial boundary and equations of motion are determined by the principle of stationary action. The quantum pressure is determined by the virial of the force resulting from the electronic momentum flux through the surface of the open system. A scaling procedure is used to demonstrate that the expectation value of the pressure–volume product of a proper open system is proportional to its surface virial. Previous work, in analogy with the classical virial theorem for a contained system, incorrectly relates the pressure to the external forces of constraint acting on a closed system. A neon vise consisting of a chain of three, four or five hydrogen molecules compressed between two neon atoms is used to introduce the quantum definition of pressure and study its effect on the mechanical properties of an atom and on the topology of the electron density. Pressures approaching 160 GPa have been calculated for the vise. The topology of the electron density and the homeomorphism it exhibits with the virial field are found to be invariant to an increase in pressure, the electron density accumulating to an ever increasing extent between all pairs of nuclei which serve as the sole attractors. The virial of the Ehrenfest force acting on the surface of a compressed molecule provides a measure of the increase in the electronic kinetic energy resulting from the applied pressure. The effects of pressure on the intra- and intermolecular bonding are discussed in terms of pressure-induced changes in the electron density and in the mechanical properties of the atoms.

Analytical derivatives of atomic zero-flux surfaces and properties of atoms in molecules with respect to external perturbations

A complete theory of the response of the atomic zero-flux surfaces to external perturbations is presented. The resulting expressions for the analytical derivatives of the properties of atoms in molecules (AIMs) are implemented in an efficient computer code. Several test calculations demonstrate the clear advantages of the new approach over methods based upon numerical differentiation. The present development opens an avenue to routine calculations of the second-order response properties of AIMs.