Atoms in molecules in real space: a fertile field for chemical bonding

In this perspective, we review some recent advances in the concept of atoms-in-molecules from a real space perspective. We first introduce the general formalism of atomic weight factors that allows unifying the treatment of fuzzy and non-fuzzy decompositions under a common algebraic umbrella. We then show how the use of reduced density matrices and their cumulants allows partitioning any quantum mechanical observable into atomic or group contributions. This circumstance provides access to electron counting as well as energy partitioning, on the same footing. We focus on how the fluctuations of atomic populations, as measured by the statistical cumulants of the electron distribution functions, are related to general multi-center bonding descriptors. Then we turn our attention to the interacting quantum atom energy partitioning, which is briefly reviewed since several general accounts on it have already appeared in the literature. More attention is paid to recent applications to large systems. Finally, we consider how a common formalism to extract electron counts and energies can be used to establish an algebraic justification for the extensively used bond order-bond energy relationships. We also briefly review a path to recover one-electron functions from real space partitions. Although most of the applications considered will be restricted to real space atoms taken from the quantum theory of atoms in molecules, arguably the most successful of all the atomic partitions devised so far, all the take-home messages from this perspective are generalizable to any real space decompositionsWe acknowledge the spanish MICINN, grant PID2021-122763NB-I00 and the FICyT, grant IDI/2021/000054 for financial support. TRR gratefully acknowledges DGTIC/UNAM for computer time (LANCAD-UNAM-DGTIC 250

DEFECT ELECTRONIC STATES IN BETA-CAROTENE AND LOWER HOMOLOGS

We present semi-empirical calculations of the atomic geometries and electronic charge distributions of beta-carotene homologues of different chain lengths. We find defects in charged and photoexcited chains that are similar to the defects found in the degenerate polymer trans-polyacetylene, and we show how confinement affects these defects as the chains we shortened. Our results exhibit a generalized form of charge-conjugation symmetry in which the properties of a negatively charged defect are related to those of a positive one and vice versa

Designing Functional Materials Driven by the Lattice Degree of Freedom

Advanced functional materials play a vital role in modern industry and human society. Therefore, accelerating the discovery and exploration of novel functional materials is critical for us as a society to tackle energy issues and further developments. In this regard, computational materials science based on quantum mechanics is now well established as a crucial pillar in condensed matter physics, chemistry, and materials science research, in addition to experiments and phenomenological theories. In this thesis, the strategy of designing new functional materials driven by the lattice degree of freedom is explored, where "lattice" refers to (1) the ground state crystal structures, (2) elementary excitations as represented by phonons, (3) coupling within themselves (i.e., anharmonicity) and the other degrees of freedom (i.e., electron-phonon interaction). We systematically studied several classes of physical phenomena and the resulting properties, such as magneto-structural coupling and magnetocalorics, anharmonicity and thermal conductivity, electron-phonon interaction and superconductivity. Additionally, an integrated computational paradigm that combines high-throughput (HTP) calculations, phonon theory, and CALPHAD methods is established and applied to design metastable functional materials, extending the applicability of DFT beyond 0 K. Considering lattice as crystal structures, we selected MAB phases with nanolaminated crystal structure as a test case, and performed an HTP screening for stable magnetic MAB compounds and predicted potential candidate magnets for permanent magnets and magnetocaloric applications. After a comprehensive validation, 21 novel compounds are predicted to be stable based on the systematic evaluation of thermodynamic, mechanical, and dynamical stabilities, and the number of stable compounds is increased to 434 taking the tolerance of convex hull being 100 meV/atom. The detailed evaluation of the magnetocrystalline anisotropy energy (MAE) and the magnetic deformations leads to 23 compounds with significant uniaxial anisotropy (MAE > 0.4 MJ/m3) and 99 systems with reasonable magnetic deformation (> 1.5 %). For those compounds containing no expensive, toxic, or critical elements, it is observed that Fe3Zn2B2 is a reasonable candidate as gap permanent magnet, and Fe4AlB4, Fe3AlB4, Fe3ZnB4, and Fe5B2 as potential magnetocaloric materials. This work paves the way for designing novel magnetic materials for energy applications based on the combinatorial sampling of the chemical space with specific crystal structure prototypes. Moreover, considering the elementary excitations of lattice vibrations, i.e., phonons, the anharmonicity caused by phonon-phonon interaction leads to many intriguing properties, such as the lattice thermal conductivity. We performed DFT calculations to evaluate the thermal transport properties of novel 2D MoSi2N4 and WSi2N4, and found their thermal conductivities being 162 W/mK and 88 W/mK at room temperature, respectively, which are 7 and 4 times the one for monolayer MoS2, 16 and 9 times the one for silicone. These results show that, MoSi2N4 and WSi2N4 have promising potential being thermal management materials. Additionally, to gain insight into the low thermal conductivity of 2D materials, we investigated the mechanism of anharmonicity from the fundamental phonon mode and electronic structure level for GaX (X= N, P, As). The thermal conductivity of GaP is calculated to be 1.52 W/mK, which is unexpectedly ultra-low and in sharp contrast to GaN and GaAs. The reason for the low thermal conductivity of the GaP can be attributed to the fact that the FA phonon dominates the thermal conductivity of GaN but contributes less to that of GaP, which is due to the symmetry-based selection rule and difference in atomic structure. The phonon anharmonicity quantified by the Grüneisen parameter is further analyzed to understand the phonon–phonon scattering, indicating the strong phonon-phonon scattering of GaP and the strongest phonon anharmonicity of GaP. The buckling structure has a strong influence on the anharmonicity, leading to low thermal conductivity. The non-bonding lone pair electrons of P and As atoms are stronger, which induces nonlinear electrostatic forces upon thermal agitation, leading to increased phonon anharmonicity in the lattice and thus reducing the thermal conductivity. Furthermore, high order phonon anharmonicity could have a significant effect on the thermal transport properties in materials within strong anharmonicity. Hence, we calculated the thermal conductivity of pristine EuTiO3. And the role of the quartic anharmonicity in the lattice dynamics and thermal transport of the cubic EuTiO3 was elucidated by combining ab initio self-consistent phonon theory with compressive sensing techniques. The anti-ferromagnetic G-type magnetic structure is used to mimic the para-magnetic EuTiO3. We find that the strong quartic anharmonicity of oxygen atoms plays an important role in the phonon quasiparticles without imaginary frequencies and causes the hardening of the vibrational frequencies of soft modes. Furthermore, in terms of electron-phonon interaction, we derived from DFT calculations the formation energies of a newly synthesized orthorhombic compound GeNCr3, which is a metastable phase. In accordance with the experimentally discovered superconductivity in antiperovskite MgCNi3, we performed calculations to evaluate the electron-phonon interaction and the resulting superconducting critical temperature of GeNCr3. It is observed that its superconducting temperature is about 8.2 K, driven by the electron-phonon interaction. Correspondingly, it is suspected that superconductivity may exist in the other MAX, MAB, and APV compounds, which will be investigated in the future based on the established workflow to evaluate the electron-phonon coupling. Such a workflow allows us to obtain the T-dependence of electric conductivities and also the lattice thermal conductivities. Last but not least, considering the thermodynamic properties where the lattice free energy plays a dominant role at the finite temperatures, we combined DFT calculations and CALPHAD modeling to optimize the phase diagrams, which can be validated with experiments and be bridged to phase field simulations to map out the processing-microstructure-property relationships. For instance, the thermodynamic properties of the Fe-Sn system are studied. First-principles phonon calculations with the quasi-harmonic approximation (QHA) approach were performed to compute the thermodynamic properties at finite temperatures. Thermodynamic properties, phonon dispersions of pure elements, and intermetallics were predicted to make up for the shortage of experimental data. A set of self-consistent thermodynamic parameters of the Fe-Sn system are obtained by the CALPHAD approach. Thermodynamic modeling of the Fe-Sn phase diagram has been re-established. The metastable phase Fe3Sn was first introduced into the current metastable phase diagram and corrected phase locations of Fe5Sn3 and Fe3Sn2 under the newly measured corrected temperature ranges. In summary, in my thesis, a systematic computational paradigm has been established based on DFT to tackle both the thermodynamic and non-equilibrium transport properties associated with the lattice degree of freedom. Such a paradigm allows us to design and optimize functional materials with physical properties driven by magneto-structural coupling, phonon-phonon coupling, and electron-phonon interaction, and also to bridge to large-scale simulations

Studies of Molecular and Cluster Fragmentation Using Synchrotron Radiation: Measurements and Models

A new spectrometer for studying photoinduced fragmentation has been designed and commissioned. The instrument produces a detailed view of the energy and angular emission of fragments, which in the case of small molecules can be related to their geometry at the moment of dissociation. The spectral profiles for single, double and triple ion coincidences are analyzed in terms of molecular alignment, and nuclear dynamics. A model based upon molecular symmetry and dipole excitation was developed for interpreting multi-coincidence spectra where all ionic fragments are measured. The basic principles of the model can be applied to higher-order fragmentation processes as well, and a picture of molecular dynamics has been obtained. In the case of molecular dissociation, anisotropy of the fragments and thus the geometry of the molecules at the moment of dissociation has been of special interest. The measurements performed on ammonia, sulfur dioxide, water, ozone and nitrogen show clear evidence of anisotropy arising from alignment upon core excitation. This provides information on the symmetry of the core excited state as well as geometry changes. The anisotropy indirectly provides information on localization/delocalization of the core excitation. Oxygen 1s to "sigma like" transitions show clear evidence for localized excitation in ozone but not in sulfur dioxide. Moreover the spectrometer is used to perform multi-coincidence studies of dynamic effects of argon cluster fragmentation. Both size and energy dependent measurements are reported. Evidence for nuclear rearrangements before fragmentation is found for small ( ~ 5) argon clusters by studying the fragmentation patterns around the argon 2p threshold. The time frame of dissociation for various cluster sizes is also presented. This in connection with a model describing the influence on the peaks shapes for dissociation on a picosecond to microsecond time scale in the spectrometer

Electron and Molecular Dynamics: Penning Ionization and Molecular Charge Transfer

An understanding of fundamental reaction dynamics is an important problem in chemistry. In this work, experimental and theoretical methods are combined to study the dynamics of fundamental chemical reactions. Molecular collision and dissociation dynamics are explored with the Penning ionization of amides, while charge transfer reactions are examined with charge transport in organic thin film devices.Mass spectra from the Penning ionization of formamide by He*, Ne*, and Ar* were measured using molecular beam experiments. When compared to 70eV electron ionization spectra, the He* and Ne* spectra show higher yields of fragments resulting from C!N and C!H bond cleavage, while the Ar* spectrum only shows the molecular ion, H-atom elimination, and decarbonylation. The differences in yields and observed fragments are attributed to the differences in the dynamics of the two ionization methods. Fragmentation in the Ar* spectrum was analyzed using quantum chemistry and RRKM calculations. Calculated yields for the Ar* spectrum are in excellent agreement with experiment and show that 15% and 50% of the yields for decarbonylation and H-atom elimination respectively are attributed to tunnelingThe effects of defects, traps, and electrostatic interactions on charge transport in imperfect organic field effect transistors were studied using course-grained Monte Carlo simulations with explicit introduction of defect and traps. The simulations show that electrostatic interactions dramatically affect the field and carrier concentration dependence of charge transport in the presence of a significant number of defects. The simulations also show that while charge transport decreases linearly as a function of neutral defect concentration, it is roughly unaffected by charged defect concentration. In addition, the trap concentration dependence on charge transport is shown to be sensitive to the distribution of trap sites.Finally, density functional theory calculations were used to study how charge localization affects the orbital energies of positively charged bithiophene clusters. These calculations show that the charge delocalizes over at least seven molecules, is more likely to localize on "tilted" molecules due to polarization effects, and affects molecules anisotropically. These results suggest that models for charge transport in organic semiconductors should be modified to account for charge delocalization and intermolecular interactions

Dressed ion-pair states of an ultralong-range Rydberg molecule

We predict the existence of a universal class of ultralong-range Rydberg molecular states whose vibrational spectra form trimmed Rydberg series. A dressed ion-pair model captures the physical origin of these exotic molecules, accurately predicts their properties, and reveals features of ultralong-range Rydberg molecules and heavy Rydberg states with a surprisingly small Rydberg constant. The latter is determined by the small effective charge of the dressed anion, which outweighs the contribution of the molecule's large reduced mass. This renders these molecules the only known few-body systems to have a Rydberg constant smaller than $R_\infty/2$.Comment: 6 pages, 3 figures and supplemental material (4 pages and 4 figures

One Scaffold, Three Binding Modes: Novel and Selective Pteridine Reductase 1 Inhibitors Derived from Fragment Hits Discovered by Virtual Screening†

The enzyme pteridine reductase 1 (PTR1) is a potential target for new compounds to treat human African trypanosomiasis. A virtual screening campaign for fragments inhibiting PTR1 was carried out. Two novel chemical series were identified containing aminobenzothiazole and aminobenzimidazole scaffolds, respectively. One of the hits (2-amino-6-chloro-benzimidazole) was subjected to crystal structure analysis and a high resolution crystal structure in complex with PTR1 was obtained, confirming the predicted binding mode. However, the crystal structures of two analogues (2-amino-benzimidazole and 1-(3,4-dichloro-benzyl)-2-amino-benzimidazole) in complex with PTR1 revealed two alternative binding modes. In these complexes, previously unobserved protein movements and water-mediated protein-ligand contacts occurred, which prohibited a correct prediction of the binding modes. On the basis of the alternative bindingmode of 1-(3,4-dichloro-benzyl)-2-amino-benzimidazole, derivatives were designed and selective PTR1 inhibitors with low nanomolar potency and favorable physicochemical properties were obtained

Molecular Dynamics Methods applied to flexible macromolecules

Cement-based materials, such as concrete or mortars, are usually considered materials with low technological level. Although they are the most employed human made materials in the world, others such as wood, plastics, metals and even stones are usually more valued in the everyday life: probably the fact that cement is cheap, readily available, common, and has been employed successfully for centuries, contributes to its low technology perception. However, this vision is far from the reality: the cement paste is a complex multicomponent and heterogeneous composite system, with different structural features at different length scales. The mechanism in which the clinker in contact with water becomes a hardened paste comprises hundreds of chemical reactions and physical processes. Understanding the molecular details of cement hydration processes is of fundamental importance due to the technological and economical impact of these materials. Several aspects need to be considered, and a realistic approach should be limited to a few specific features. Many efforts have been devoted over the last 40 years to develop mathematical models for understanding and predicting highly complex cement hydration kinetics, microstructure development and the implications of these for the changing physical-chemical properties of cement paste and concrete. An accurate hydration simulation approach would enable scientists and engineers not only to predict the performance of concrete, but also to design new cementitious materials. Despite significant effort and progress, the ability to perform such a complete simulation has not yet been developed, mainly because cement hydration is one of the more complex phenomena in engineering/materials science. The main objective of this PhD thesis is to analyse the influence of superplasticizers on the microevolution of cement suspensions during early hydration based of Molecular Dynamics (MD) approaches. To this purpose we implemented a MD protocol for the study of the behavior of polycarboxylate-ether-based superplasticizers (PCEs) in the presence of selected cement surfaces, tricalcium aluminate (C3A) and tricalcium silicate (C3S), water molecules and calcium hydroxide. The final goal of the project, which was carried in collaboration with the group of Prof. G. Artioli - Università degli Studi di Padova, Dipartimento di Geoscienze, was to clarify structure-properties relationships, in order to design new products with enhanced properties. In fact, the rheology of cement pastes can be controlled by the use of superplasticizers that, by adsorbing on the surfaces of cement particles, enhance their workability. The protocol was made up of the following steps: i) building of the cement surfaces, ii) parameterization of force field, iii) setting of the simulation and evaluation of physical observables. Some methodological knowledges acquired were employed on side-applications, for example the evaluation of electrostatic interactions of other organic molecules, in particular partial charges of amino acids (AA) and nonstandard amino acids (Non-AA), present in the human Connexin protein. To be precise, following the earlier approach of Bayly et al [Bayly1993], we obtained the charge set by fitting to the electrostatic potentials of Non-AA calculated using ab-initio methods. This effort was carried out in collaboration with the group of F. Mammano - Università degli Studi di Padova, Dipartimento di Fisica e Astronomia [Zonta2014]. Finally, in a joint effort with Dott.ssa L. Orian, Dott. M. Torsello and P. Calligari, of my research group, simulate complete simulation was carried out of the Connexin 26 hemichannel (Cx26) behaviour in the presence of post-translational modifications (PTMs) and Ca2+. The contribution to this joint project described in this thesis, was aimed to i) the analysis of the structure of the channel and ii) the preservation of salt bridges between Glu47, Arg75 and gamma-Glu47, Arg75 in the presence/asbsence of Ca2+. Lastly, preliminary results based on a collaboration with Stazione Sperimentale del Vetro (SSV) of Murano (Ve) for the project: "Computational methods for the modeling of equilibrium properties of glassy materials", is presented. The goal of this work was the elaboration, optimization and validation of a model of the type of ideal solutions for the thermodynamic properties of glasses and the inclusion in integrated software platforms. This work is organised as follows. In chapter 1, a brief overview is presented of the atomistic simulation methods used during the Thesis, because several levels of theory were selected depending on their capabilities to solve punctual problems: ab initio, Molecular Mechanics, and Molecular Dynamics. In chapter 2, an introduction to cement chemistry and the necessary basis is given in order to follow the results and discussions of the systems presented in this Thesis. It covers a description of clinker phases, superplasticizers, the hydration process, the cement paste structure and computational methods applied in cement research. In chapter 3, the results of four MD simulations are discussed for a system consisting of PCE-(23-7-1), a comb-shaped polymer unit model superplasticizer of methyl-polyethylene glycole methacrylate and methacrylic acids (seven back bone units, one side-chain unit and twenty three polyethylene-oxide units in the side chain), the C3A and C3S surfaces, explicit molecules of water, Ca2+ and OH- ions (pore solution): from the MD trajectories were calculated conformational properties. In chapter 4, the results are discussed of partial charges parametrization of Non-AA, the structural channel analysis and salt-bridges analysis of Cx26 protein. In chapter 5, the thermodynamic model is presented for calculating the composition of glasses, the interpolation for temperature dependence of thermodynamic properties and the validation of model with a simple binary oxide system Na2O-SiO2

Molecular orbital theory: an introductory lecture note and reprint volume

These notes are based on lectures on molecular orbital theory that we have presented at the University of Copenhagen and Columbia University. They were designed primarily for advanced-undergraduate and first-year graduate students as an introduction to molecular orbital theory. It is apparent that the molecular orbital theory is a very useful method of classifying the ground and excited states of small molecules. The transition metal complexes occupy a special place here, and the last chapter is devoted entirely to this subject. We believe that modern inorganic chemists should be acquainted with the methods of the theory, and that they will find approximate one-electron calculations as helpful as the organic chemists have found simple Hückel calculations. For this reason, we have included a calculation of the permanganate ion in Chapter 8. On the other hand, we have not considered conjugated pi systems because they are excellently discussed in a number of books. Our intuitive approach in the use of symmetry methods is admittedly nonrigorous and therefore will be unsatisfactory to purists, but we believe this is the best way to introduce symmetry ideas to the majority of students. Once the student has learned how to use symmetry methods, it will be easier for him to appreciate more formal and rigorous treatments. Several reprints of papers on molecular orbital theory are included in the back of the book. The papers treat a substantial number of the important molecular geometries. The reader should be able to follow the discussions after reading through the lecture notes. We thank our colleagues in New York and Copenhagen for help with the manuscript. We gratefully acknowledge the help of Dr. Arlen Viste and Mr. Harold Basch in preparing Appendix 8-B. Finally, it is a pleasure to acknowledge the expert assistance of Mrs. Diane Celeste in preparing the final manuscript. C. J. BALLHAUSEN, Kobenhavn HARRY B. GRAY, New York October 196