Properties of atoms in molecules: additivity and transferability of group polarizabilities

Synergistic modification of hot-melt extrusion and nobiletin on the multi-scale structures, interactions, thermal properties, and in vitro digestibility of rice starch

Background

Rice starch has high digestibility due to its large carbohydrate content. Synergistic modification of hot-melt extrusion (HME) and additives such as flavonoids, hydrocolloids, proteins, lipids, and other additives has the tendency to retard the rate of starch hydrolysis. Hence, the current investigation aimed to study the combined effect of the HME-assisted addition of nobiletin (NOB, 0, 2, 4, and 6%) on the multi-scale structures, interactions, thermal, and digestibility characteristics of rice starch.

Methods

The study employed density functional theory calculations and an infrared second derivative of an Fourier-transform infrared (FTIR) spectrometer to analyze the interactions between NOB and starch. The physicochemical properties of the starch extrudates were characterized by FTIR, 13C nuclear magnetic resonance, X-ray diffraction, and differential scanning calorimetry, while the digestibility was evaluated using an in vitro digestion model.

Results

HME was found to disrupt the crystalline structure, helix structure, short-ordered structure, and thermal properties of starch. The interaction between NOB and starch involved hydrophobic interactions and hydrogen bonds, effectively preventing the molecular chains of starch from interacting with each other and disrupting their double helix structure. The addition of NOB led to the formation of a highly single-helical V-type crystalline structure, along with the formation of ordered structural domains. Consequently, the combined treatment significantly enhanced the ordered structure and thermal stability of starch, thus effectively leading to an increase in resistant starch and slowly digestion starch.

Discussion

The study underscores that synergistic modification of HME and NOB holds promise for enhancing both the nutritional value and functional properties of rice starch. These findings offer valuable insights for developing high-quality rice starch products with broader applications.

The electron density: a fidelity witness for quantum computation

There is currently no combination of quantum hardware and algorithms that can provide an advantage over conventional calculations of molecules or materials. However, if or when such a point is reached, new strategies will be needed to verify predictions made using quantum devices. We propose that the electron density, obtained through experimental or computational means, can serve as a robust benchmark for validating the accuracy of quantum computation of chemistry. An initial exploration into topological features of electron densities, facilitated by quantum computation, is presented here as a proof of concept. Additionally, we examine the effects of constraining and symmetrizing measured one-particle reduced density matrices on noise-driven errors in the electron density distribution. We emphasize the potential benefits and future need for high-quality electron densities derived from diffraction experiments for validating classically intractable quantum computations of materials.

Evolution of microstructures and hydrogen bond interactions within choline amino acid ionic liquid and water mixtures

The microstructures and interactions of choline amino acid ([Cho][AA]) ionic liquid (IL) and water molecules were investigated. When water was added to [Cho][AA], the asymmetric and symmetric vibration peaks of the -COO^- group shifted to lower and higher wavenumbers, respectively. The increase of water addition also resulted in increased conductivity values and decreased viscosity values of [Cho][AA]-water mixtures. These features are consistent with the physical picture that [Cho][AA] could gradually dissociate into hydrated tight ion pairs and water-separated ion pairs and then into free and solvated ions. When it comes to different anions (choline lysine, [Cho][Lys], and choline aspartic acid, [Cho][Asp]), the anion structure has a significant regulation on [Cho][AA]-water interactions. The shorter side chain length and strong polar -COOH group of Asp^- endow [Cho][Asp] with stronger cation-anion interactions and less dissociation by water molecules. As a result, the frequency shift degrees and conductivity values of [Cho][Asp]-water mixtures were lower, and the viscosity values were higher than those of [Cho][Lys]-water mixtures. And, [Cho][Lys] could completely dissociate as free hydrated ions at w : IL ≥ 7 : 3, while the free hydrated ions of [Cho][Asp] only occurred when the w : IL ratio reached 8 : 2. These results can ease the experimental effort and improve the application efficiency of [Cho][AA] ILs.

The Dielectric Behavior of Protected HKUST-1

We investigated the adsorption properties and the dielectric behavior of a very well-known metal-organic framework (MOF), namely Cu3(BTC)2 (known as HKUST-1; BTC = 1,3,5-benzenetricarboxylate), before and after protection with some amines. This treatment has the purpose of reducing the inherent hygroscopic nature of HKUST-1, which is a serious drawback in its application of as low-dielectric-constant (low-κ) material. Moreover, we investigated the structure of HKUST-1 under a strong electric field, confirming the robustness of the framework. Even under dielectric perturbation, the water molecules adsorbed by the MOF remained almost invisible to X-ray diffraction, apart from those directly bound to the metal ions. However, the replacement of H2O with a more visible guest molecule such as CH2Br2 made the cavity that traps the guest more visible. Finally, in this work we demonstrate that impedance spectroscopy is a valuable tool for identifying water sorption in porous materials, providing information that is complementary to that of adsorption isotherms.

Ultrafast Vibrational Response of Activated C-D Bonds in a Chloroform-Platinum(II) Complex

The vibrational response of the activated C-D bond in the chloroform complex [Pt(C₆H₅)₂(btz-N,N')·CDCl₃, where btz = 2,2'-bi-5,6-dihydro-4H-1,3-thiazine] is studied by linear and nonlinear two-dimensional infrared (2D-IR) spectroscopy. The change of the C-D stretching vibration of metal-coordinated CDCl₃ relative to the free solvent molecule serves as a measure of the non-classical Pt···D-C interaction strength. The stretching absorption band of the activated C-D bond displays a red shift of 119 cm^-1 relative to uncoordinated CDCl₃, a strong broadening, and an 8-fold enhancement of spectrally integrated absorption. The infrared (IR) absorption and 2D-IR line shapes are governed by spectral diffusion on 200 fs and 2 ps time scales, induced by the fluctuating solvent CDCl₃. The enhanced vibrational absorption and coupling to solvent forces are assigned to the enhanced electric polarizability of the activated C-D bond. Density functional theory calculations show a significant increase of C-D bond polarizability of CDCl₃ upon coordination to the 16 valence electron Pt(II) complex.

A fast approximate extension of the interacting quantum atoms energy decomposition to excited states

An approach is developed for the fast calculation of the interacting quantum atoms energy decomposition (IQA) from the information contained in the first order reduced density matrix only. The proposed methodology utilizes an approximate exchange-correlation density from Density Matrix Functional Theory without the need to evaluate the correlation-exchange contribution directly. Instead, weight factors are estimated to decompose the exact V_xc into atomic and pairwise contributions. In this way, the sum of the IQA contributions recovers the energy obtained from the electronic structure calculation. This method can, hence, be applied to obtain atomic contributions in excited states on the same footing as in their ground states using any method that delivers the reduced first-order density matrix. In this way, one can locate chromophores from first principles quantum chemical calculations. Test calculations on the ground and excited states of a set of small molecules indicate that the scaled atomic contributions reproduce vertical electronic transition energies calculated exactly. This approach may be useful to extend the applicability of the IQA approach in the study of large photochemical systems especially when the calculations of the second order reduced density matrices is prohibitive or not possible.

The effect of cation-π interactions on the stability and electronic properties of anticancer drug Altretamine: a theoretical study

The present work utilizes density functional theory (DFT) calculations to study the influence of cation-π interactions on the electronic properties of the complexes formed by Altretamine [2,4,6-tris(dimethylamino)-1,3,5-triazine], an anticancer drug, with mono- and divalent (Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺ and Ca²⁺) metal cations. The structures were optimized with the M06-2X method and the 6-311++G(d,p) basis set in the gas phase and in solution. The theory of `Atoms in Molecules' (AIM) was applied to study the nature of the interactions by calculating the electron density ρ(r) and its Laplacian at the bond critical points. The charge-transfer process during complexation was evaluated using natural bond orbital (NBO) analysis. The results of DFT calculations demonstrate that the strongest/weakest interactions belong to Be²⁺/K⁺ complexes. There are good correlations between the achieved densities and the amounts of charge transfer with the interaction energies. Finally, the stability and reactivity of the cation-π interactions can be determined by quantum chemical computation based on the molecular orbital (MO) theory.

Toward universal substituent constants: Model chemistry sensitivity of descriptors from the quantum theory of atoms in molecules

The quantum theory of atoms in molecules (QTAIM) provides a theoretical foundation to determine the properties of functional groups through additive atomic contributions. Many studies have used QTAIM in their analyses with a variety of electronic structure methods, but it is unknown if the properties measured using one model chemistry, the combination of the electronic structure method and basis set, can be compared to those measured by another. Here, we evaluate the sensitivity of QTAIM functional group and bond critical point properties using six functionals and seven basis sets. High-level B2PLYPD3-BJ/aug-cc-pV5Z reference values are provided for 116 functional groups and the property sensitivity with respect to these values are evaluated based on absolute deviations and by assessing linear relationships. Functional group properties, including charges, dipoles, quadrupoles and volumes, were found to be mostly insensitive to choice of computational model chemistry. However, due to structural and topological inconsistencies, the 6-31G(d) basis set is not recommended for use. Bond critical point properties varied with choice of model chemistry, but models incorporating hybrid functionals and triple-ζ basis sets provided values suitable for use in regression studies.

Van der Waals forces in free and wetting liquid films

Van der Waals interactions induced by fluctuations of electromagnetic field bear universal nature and act between individual atoms, condensed particles or bodies of any type. Continuously growing interest to theoretical understanding as well as to precise evaluation of van der Waals forces is caused by their fundamental role in many physical, chemical, and biological processes. In this paper, we scrutinize progress in the studies of van der Waals forces, related to recent active development of Coupled Dipole Method (CDM) for the analysis of the behavior and properties of nanosized systems. The application of CDM for the analysis of thin liquid films allowed achieving substantial progress in understanding the behavior of free and wetting films. It was shown that both the macroscopic properties, such as excess free energy and Hamaker constants and the local microscopic parameters, such as polarizabilities, can be successfully calculated based only on properties of individual molecules. The impact of lateral film confinement on the specific excess free energy and the film stability was elucidated, and effect of spatial constraints on the spectrum of vibrational states for liquid film and the underlying substrate was analyzed. It was shown that van der Waals interactions between molecules represent the universal mechanism for dynamic structuring and formation of boundary layers and that the CDM allows self-consistently calculating the properties of these layers in both solid and liquid phases.

New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 1. Theory and accuracy

A new method was developed to compute atom-in-material polarizabilities and dispersion coefficients for diverse material types.

Partition of optical properties into orbital contributions

A new tool to analyze the response property through the partition of nonlinear optical properties in terms of orbital contributions (PNOC), valuable in the assessment of the electronic structure methods in the NLOPs computations, is presented.

Quantum mechanical determination of atomic polarizabilities of ionic liquids

We present an accurate and simple quantum mechanical methodology to calculate atomic polarizabilities of charged species.

Modeling adsorbate-induced property changes of carbon nanotubes

Because of their potential for chemical functionalization, carbon nanotubes (CNTs) are promising candidates for the development of devices such as nanoscale sensors or transistors with novel gating mechanisms. However, the mechanisms underlying the property changes due to functionalization of CNTs still remain subject to debate. Our goal is to reliably model one possible mechanism for such chemical gating: adsorption directly on the nanotubes. Within a Kohn-Sham density functional theory framework, such systems would ideally be described using periodic boundary conditions. Truncating the tube and saturating the edges in practice often offers a broader selection of approximate exchange-correlation functionals and analysis methods. By comparing the two approaches systematically for NH₃ and NO₂ adsorbates on semiconducting and metallic CNTs, we find that while structural properties are less sensitive to the details of the model, local properties of the adsorbate may be as sensitive to truncation as they are to the choice of exchange-correlation functional, and are similarly challenging to compute as adsorption energies. This suggests that these adsorbate effects are nonlocal. © 2017 Wiley Periodicals, Inc.

GenLocDip: A Generalized Program to Calculate and Visualize Local Electric Dipole Moments

Local dipole moments (i.e., dipole moments of atomic or molecular subsystems) are essential for understanding various phenomena in nanoscience, such as solvent effects on the conductance of single molecules in break junctions or the interaction between the tip and the adsorbate in atomic force microscopy. We introduce GenLocDip, a program for calculating and visualizing local dipole moments of molecular subsystems. GenLocDip currently uses the Atoms-In-Molecules (AIM) partitioning scheme and is interfaced to various AIM programs. This enables postprocessing of a variety of electronic structure output formats including cube and wavefunction files, and, in general, output from any other code capable of writing the electron density on a three-dimensional grid. It uses a modified version of Bader's and Laidig's approach for achieving origin-independence of local dipoles by referring to internal reference points which can (but do not need to be) bond critical points (BCPs). Furthermore, the code allows the export of critical points and local dipole moments into a POVray readable input format. It is particularly designed for fragments of large systems, for which no BCPs have been calculated for computational efficiency reasons, because large interfragment distances prevent their identification, or because a local partitioning scheme different from AIM was used. The program requires only minimal user input and is written in the Fortran90 programming language. To demonstrate the capabilities of the program, examples are given for covalently and non-covalently bound systems, in particular molecular adsorbates. © 2016 Wiley Periodicals, Inc.

Local electric dipole moments: A generalized approach

We present an approach for calculating local electric dipole moments for fragments of molecular or supramolecular systems. This is important for understanding chemical gating and solvent effects in nanoelectronics, atomic force microscopy, and intensities in infrared spectroscopy. Owing to the nonzero partial charge of most fragments, "naively" defined local dipole moments are origin-dependent. Inspired by previous work based on Bader's atoms-in-molecules (AIM) partitioning, we derive a definition of fragment dipole moments which achieves origin-independence by relying on internal reference points. Instead of bond critical points (BCPs) as in existing approaches, we use as few reference points as possible, which are located between the fragment and the remainder(s) of the system and may be chosen based on chemical intuition. This allows our approach to be used with AIM implementations that circumvent the calculation of critical points for reasons of computational efficiency, for cases where no BCPs are found due to large interfragment distances, and with local partitioning schemes other than AIM which do not provide BCPs. It is applicable to both covalently and noncovalently bound systems. © 2016 Wiley Periodicals, Inc.

DAMQT 2.1.0: A new version of the DAMQT package enabled with the topographical analysis of electron density and electrostatic potential in molecules

DAMQT-2.1.0 is a new version of DAMQT package which includes topographical analysis of molecular electron density (MED) and molecular electrostatic potential (MESP), such as mapping of critical points (CPs), creating molecular graphs, and atomic basins. Mapping of CPs is assisted with algorithmic determination of Euler characteristic in order to provide a necessary condition for locating all possible CPs. Apart from the mapping of CPs and determination of molecular graphs, the construction of MESP-based atomic basin is a new and exclusive feature introduced in DAMQT-2.1.0. The GUI in DAMQT provides a user-friendly interface to run the code and visualize the final outputs. MPI libraries have been implemented for all the tasks to develop the parallel version of the software. Almost linear scaling of computational time is achieved with the increasing number of processors while performing various aspects of topography. A brief discussion of molecular graph and atomic basin is provided in the current article highlighting their chemical importance. Appropriate example sets have been presented for demonstrating the functions and efficiency of the code.

Exploring the Gradient Paths and Zero Flux Surfaces of Molecular Electrostatic Potential

The gradient vector field of molecular electrostatic potential, ∇V(r), has remained relatively unexplored in molecular quantum mechanics. The present article explores the conceptual as well as practical aspects of this vector field. A three-dimensional atomic partition of molecular space has been achieved on the basis of zero flux surfaces (ZFSs) of ∇V(r). Such ZFSs may completely enclose some of the atoms in the molecule, unlike what is observed in density-based atomic partitioning. The demonstration of this phenomenon is elucidated through typical examples, e.g., N2, CO, H2O, H2CO, OF(•), :CH2, and NH3BF3, where the electronegative atoms or group of atoms (group electronegativity) exhibits a closed ZFS of ∇V(r) around them. The present article determines an explicit reason for this phenomenon and also provides a necessary and sufficient condition for such a closed ZFS of ∇V(r) to exist. It also describes how the potential-based picture of atoms in molecules differs from its electron density-based analogue. This work further illustrates the manifestation of anisotropy in the gradient paths of MESP of some molecular systems, with respect to CO, (•)OH, H2O, and H2CO, and points to its potential in understanding the reactivity patterns of the interacting molecules.

Introducing DDEC6 atomic population analysis: part 1. Charge partitioning theory and methodology

We introduce a new atomic population analysis method that performs exceptionally well across an extremely broad range of periodic and non-periodic material types.

Distributed polarizability models for imidazolium-based ionic liquids

Quantum chemical calculations are used to derive distributed polarizability models sufficiently accurate and compact to be used in classical molecular dynamics simulations of imidazolium-based room temperature ionic liquids. Two distributed polarizability models are fitted to reproduce the induction energy of three imidazolium cations (1,3-dimethyl-, 1-ethyl-3-methyl-, and 1-butyl-3-methylimidazolium) and four anions (tetrafluoroborate, hexafluorophosphate, nitrate, and thiocyanate) polarized by a point charge located successively on a grid of surrounding points. The first model includes charge-flow polarizabilities between first-neighbor atoms and isotropic dipolar polarizability on all atoms (except H), while the second model includes anisotropic dipolar polarizabilities on all atoms (except H). For the imidazolium cations, particular attention is given to the transferability of the distributed polarizability sets. The molecular polarizability and its anisotropy rebuilt by the distributed models are found to be in good agreement with the exact ab initio values for the three cations and 23 additional conformers of 1-ethyl-3-methyl-, 1-butyl-3-methyl-, 1-pentyl-3-methyl-, and 1-hexyl-3-methylimidazolium cations.

Modeling biophysical and biological properties from the characteristics of the molecular electron density, electron localization and delocalization matrices, and the electrostatic potential

The electron density and the electrostatic potential are fundamentally related to the molecular hamiltonian, and hence are the ultimate source of all properties in the ground- and excited-states. The advantages of using molecular descriptors derived from these fundamental scalar fields, both accessible from theory and from experiment, in the formulation of quantitative structure-to-activity and structure-to-property relationships, collectively abbreviated as QSAR, are discussed. A few such descriptors encode for a wide variety of properties including, for example, electronic transition energies, pK(a)'s, rates of ester hydrolysis, NMR chemical shifts, DNA dimers binding energies, π-stacking energies, toxicological indices, cytotoxicities, hepatotoxicities, carcinogenicities, partial molar volumes, partition coefficients (log P), hydrogen bond donor capacities, enzyme-substrate complementarities, bioisosterism, and regularities in the genetic code. Electronic fingerprinting from the topological analysis of the electron density is shown to be comparable and possibly superior to Hammett constants and can be used in conjunction with traditional bulk and liposolubility descriptors to accurately predict biological activities. A new class of descriptors obtained from the quantum theory of atoms in molecules' (QTAIM) localization and delocalization indices and bond properties, cast in matrix format, is shown to quantify transferability and molecular similarity meaningfully. Properties such as "interacting quantum atoms (IQA)" energies which are expressible into an interaction matrix of two body terms (and diagonal one body "self" terms, as IQA energies) can be used in the same manner. The proposed QSAR-type studies based on similarity distances derived from such matrix representatives of molecular structure necessitate extensive investigation before their utility is unequivocally established.

PolaBer: a program to calculate and visualize distributed atomic polarizabilities based on electron density partitioning

This paper describes the program PolaBer, which calculates atomic polarizability tensors from electric field perturbations of a partitioned electron density distribution. Among many possible partitioning schemes, PolaBer is currently using the quantum theory of atoms in molecules and it is interfaced to programs that apply such a partitioning. The calculation of the atomic tensors follows the idea suggested by Keith [The Quantum Theory of Atoms in Molecules: From Solid State to DNA and Drug Design, (2007), edited by C. F. Matta & R. J. Boyd. Weinheim: Wiley-VCH], which enables the removal of the intrinsic origin dependence of the atomic charge contributions to the molecular dipole moment. This scheme allows the export, within chemically equivalent functional groups, of properties calculated from atomic dipoles, such as for example the atomic polarizabilities. The software permits visualization of the tensors and calculation of straightforward optical properties of a molecule (like the molar refractive index) or a crystal (assuming the molecule in a given crystal lattice).

QTAIM investigation of the electronic structure and large Raman scattering intensity of bicyclo-[1.1.1]-pentane

Our previous studies of the variation of Raman scattering intensities in saturated hydrocarbons have identified a number of structural descriptors that correlate with calculated polarizability derivatives for particular bond displacements: ring strain, steric hindrance, and alignment and location of a C-H group within the molecular framework (e.g., endo-/exo-, axial/equatorial, in-plane/out-of-plane). The bridgehead C-H bond intensities in bicyclo-[1.1.1]-pentane appear to be extraordinarily large, given its size and structure. Molecular polarizability and derivatives are analyzed here for bicyclo-[1.1.1]-pentane and propane, with HF, MP2, CCSD, B3LYP, M06, and M062X levels of theory and the Dunning AVTZ basis set. Analyses of calculated electronic charge densities were performed with two implementations of QTAIM, including an origin-dependent method and an implementation with origin-independent atomic moments. Numerically accurate atomic partitioning of mean molecular polarizabilities is achievable with either; however, accurate partitioning of polarizability derivatives places stringent requirements on the numerical integration, more so for this highly strained bicyclic structure. QTAIM reveals that most of the polarizability (~90%) can be attributed to charge transfer between atomic basins. Calculated Raman intensities are in accord with our experimental data, notably in the prediction of large trace scattering intensities for stretching of the bridgehead CH in bicyclo-[1.1.1]-pentane and for the methyl in-plane C-H in propane. Density difference plots illustrate the effects of bond displacements on the electron densities and the resultant changes in polarizability. Stretching of the bridgehead C-H bond in bicyclo-[1.1.1]-pentane produces electron density changes that are similar to those encountered upon stretching the methyl in-plane C-H of propane.

Electron-density descriptors as predictors in quantitative structure--activity/property relationships and drug design

The use of electron density-based molecular descriptors in drug research, particularly in quantitative structure--activity relationships/quantitative structure--property relationships studies, is reviewed. The exposition starts by a discussion of molecular similarity and transferability in terms of the underlying electron density, which leads to a qualitative introduction to the quantum theory of atoms in molecules (QTAIM). The starting point of QTAIM is the topological analysis of the molecular electron-density distributions to extract atomic and bond properties that characterize every atom and bond in the molecule. These atomic and bond properties have considerable potential as bases for the construction of robust quantitative structure--activity/property relationships models as shown by selected examples in this review. QTAIM is applicable to the electron density calculated from quantum-chemical calculations and/or that obtained from ultra-high resolution x-ray diffraction experiments followed by nonspherical refinement. Atomic and bond properties are introduced followed by examples of application of each of these two families of descriptors. The review ends with a study whereby the molecular electrostatic potential, uniquely determined by the density, is used in conjunction with atomic properties to elucidate the reasons for the biological similarity of bioisosteres.

Topological partition of the elastic constants of crystals

We present a partitioning of the elastic constants of a crystal into atomic contributions by using the atomic basin concept inherent to Bader's Quantum Theory of Atoms in Molecules. The partition is made by following the evolution of the cell volume and the atomic basin volumes under appropriately defined cell deformations. The method is carefully examined, including internal consistency checks. The transferability of atomic contributions between different crystals is determined by obtaining and comparing the oxygen contribution to the elastic constants of a selection of cubic oxides that includes the rock-salt, perovskite, antifluorite, and cuprite crystal families.

Energy additivity in branched and cyclic hydrocarbons

This paper considers the degree to which branched hydrocarbons obey a group additivity scheme for energy and population, extending the study of the known experimental and theoretical transferability of the methyl and methylene groups of the linear hydrocarbons. The chemical groups are defined and their properties are determined using the quantum theory of atoms in molecules (QTAIM). The calculations are carried out with a large basis set at the restricted Hartree–Fock and MP2(full) levels of theory. The deviations from additivity, noted for small ring hydrocarbons leading to the definition of strain energy, are also investigated, showing that the QTAIM energies recover the experimental values. The particular delocalization of the electron density over the surface of the cyclopropane ring, responsible for its “homoaromatic” properties, is discussed in some detail. The calculations reported here satisfy the virial theorem as required for the atomic definition of energy. The problems associated with the use of DFT theory arising from its failure to satisfy the virial theorem are discussed with reference to the study of group transferability.