Quantum chemical package Jaguar: A survey of recent developments and unique features

This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar's scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar's development in more than thirty years of its existence.

CRYSTAL23: A Program for Computational Solid State Physics and Chemistry

The Crystal program for quantum-mechanical simulations of materials has been bridging the realm of molecular quantum chemistry to the realm of solid state physics for many years, since its first public version released back in 1988. This peculiarity stems from the use of atom-centered basis functions within a linear combination of atomic orbitals (LCAO) approach and from the corresponding efficiency in the evaluation of the exact Fock exchange series. In particular, this has led to the implementation of a rich variety of hybrid density functional approximations since 1998. Nowadays, it is acknowledged by a broad community of solid state chemists and physicists that the inclusion of a fraction of Fock exchange in the exchange-correlation potential of the density functional theory is key to a better description of many properties of materials (electronic, magnetic, mechanical, spintronic, lattice-dynamical, etc.). Here, the main developments made to the program in the last five years (i.e., since the previous release, Crystal17) are presented and some of their most noteworthy applications reviewed.

The effect of long-range interactions on the infrared and Raman spectra of aragonite (CaCO3, Pmcn) up to 25 GPa

Long-range interactions are relevant in the physical description of materials, even for those where other stronger bonds give the leading contributions. In this work, we demonstrate this assertion by simulating the infrared and Raman spectra of aragonite, an important calcium carbonate polymorph (space group Pmcn) in geological, biological and materials science fields. To this aim, we used Density Functional Theory methods and two corrections to include long-range interactions (DFT-D2 and DFT-D3). The results were correlated to IR spectroscopy and confocal Raman spectrometry data, finding a very good agreement between theory and experiments. Furthermore, the evolution of the IR/Raman modes up to 25 GPa was described in terms of mode-Grüneisen's parameters, which are useful for geological and materials science applications of aragonite. Our findings clearly show that weak interactions are of utmost importance when modelling minerals and materials, even when they are not the predominant forces.

Thermodynamic Properties of Crystalline Cellulose Allomorphs Studied with Dispersion-Corrected Density Functional Methods

The phonon properties and thermodynamics of four crystalline cellulose allomorphs, Iα, Iβ, II, and III1, have been investigated using dispersion-corrected density functional theory (DFT). In line with experimental findings, the free energy differences between the studied cellulose allomorphs are small, less than 1 kJ/mol per atom. The calculated specific heat at constant volume (Cv) has been compared with the available experimental data in the temperature range 10–300 K. Quasiharmonic approximation has been employed to study thermodynamics and specific heat at constant pressure (Cp). For the studied temperature range of 10–400 K, the specific heat of all cellulose allomorphs shows very similar behavior. The calculated and experimental specific heat agree well at low temperatures below 100 K, but the deviation between theory and experiment increases with temperature. This may be due to increasing phonon anharmonicity as the temperature increases.

Anharmonic Coupling of Stretching Vibrations in Ice: A Periodic VSCF and VCI Description

The anharmonicity of O-H stretching vibrations of water ice is characterized by use of a periodic implementation of the vibrational self-consistent field (VSCF) and vibrational configuration interaction (VCI) methods, which take phonon-phonon couplings explicitly into account through numerical evaluation of high-order terms of the nuclear potential. The low-temperature, proton-ordered phase of water ice (namely, ice XI) is investigated. The net effect of a coupled anharmonic treatment of stretching modes is not just a rigid blue-shift of the respective harmonic spectral frequencies but rather a complex change of their relative spectral positions, which cannot be captured by simple scaling strategies based on harmonic calculations. The adopted techniques allow for a hierarchical treatment of anharmonic terms of the nuclear potential, which is key to an effective identification of leading factors. We show that the anharmonic independent-mode approximation─only describing the "intrinsic anharmonicity" of the O-H stretches─is unable to capture the correct physics, and that couplings among O-H stretches must be described. Inspection of harmonic normal coordinates allows identification of specific features of the O-H stretching motions which most likely enable strong mode-mode couplings. Finally, by coupling O-H stretches to all other possible modes of ice XI (THz collective vibrations, molecular librations, bendings), we identify specific types of motion which significantly affect O-H stretching states: in particular, molecular librations are found to affect the stretching states more than molecular bendings.

QUANTAS: a Python software for the analysis of thermodynamics and elastic behavior of solids from ab initio quantum mechanical simulations and experimental data

This paper presents QUANTAS, an open-source Python-based software aimed at providing a fast, flexible and easy-to-use framework to calculate the thermodynamics and elastic properties of crystalline solids. QUANTAS could be of use for researchers involved in various fields of solid-state chemistry, physics and mineralogy.

Mineralogy, petrology and materials science are fundamental disciplines not only for the basic knowledge and classification of solid phases but also for their technological applications, which are becoming increasingly demanding and challenging. Characterization and design of materials are of utmost importance and usually need knowledge of the thermodynamics and mechanical stability of solids. Alongside well known experimental approaches, in recent years the advances in both quantum mechanical methods and computational power have placed theoretical investigations as a complementary useful and powerful tool in this kind of study. In order to aid both theoreticians and experimentalists, an open-source Python-based software, QUANTAS, has been developed. QUANTAS provides a fast, flexible, easy-to-use and extensible platform for calculating the thermodynamics and elastic behavior of crystalline solid phases, starting from both experimental and ab initio data.

Thermoelasticity of Flexible Organic Crystals from Quasi-harmonic Lattice Dynamics: The Case of Copper(II) Acetylacetonate

A computationally affordable approach, based on quasi-harmonic lattice dynamics, is presented for the quantum-mechanical calculation of thermoelastic moduli of flexible, stimuli-responsive, organic crystals. The methodology relies on the simultaneous description of structural changes induced by thermal expansion and strain. The complete thermoelastic response of the mechanically flexible metal-organic copper(II) acetylacetonate crystal is determined and discussed in the temperature range 0-300 K. The elastic moduli do not just shrink with temperature but they do so anisotropically. The present results clearly indicate the need for an explicit account of thermal effects in the simulation of mechanical properties of elastically flexible organic materials. Indeed, predictions from standard static calculations on this flexible metal-organic crystal are off by up to 100%.

Thermodynamic and thermoelastic data of georesources raw minerals: Zinc sulphide and apatite

This article reports a dataset on the thermodynamic and elastic properties of two important raw minerals exploited in georesources and ore mining. The presented data refers to two zinc sulphide polymorphs, namely zinc-blende (low-pressure polymorph, space group F 4 - 3 m ) and rock-salt (high-pressure polymorph, space group F m 3 - m ) [1], and of type-A carbonated apatite, [CAp, Ca10(PO4)6CO3, space group P1] [2]. The data here reported were calculated from ab initio quantum mechanical simulations at the DFT/B3LYP level, all-electron Gaussian-type orbitals basis sets and from the analysis of the phonon properties of the zinc sulphide polymorphs and of type-A CAp by means of the quasi-harmonic approximation. In addition, a correction to take into account the effects of dispersive forces was considered to obtain the dataset of type-A carbonated apatite. This dataset, which was validated against experimental thermodynamic data reported in literature, has been employed to construct the phase diagram between the two zinc sulphide polymorphs and discuss their stability over the temperature and pressure range 0-800 K and 0-25 GPa. The thermodynamic and thermoelastic data of CAp were obtained between 0 and 600 K and 0-3 GPa, below the temperature of thermal decomposition of the mineral. The reported data can be of use in several application fields, for instance fundamental georesource exploration and exploitation, and also in applied mineralogy, geology, material science, and as a reference to assess the quality of other theoretical approaches. Furthermore, the data of type-A carbonated apatite could be useful for designing and processing new biomaterials with tailored properties.

Thermo-Elasticity of Materials from Quasi-Harmonic Calculations

An effective algorithm for the quasi-harmonic calculation of thermo-elastic stiffness constants of materials is discussed and implemented into the Crystal program for quantum-mechanical simulations of extended systems. Two different approaches of increasing complexity and accuracy are presented. The first one is a quasi-static approximation where the thermal dependence of elastic constants is assumed to be due only to the thermal expansion of the system. The second one is fully quasi-harmonic, takes into account thermal expansion, and explicitly computes Helmholtz free energy derivatives with respect to strain. The conversion of isothermal into adiabatic thermo-elastic constants is also addressed. The algorithm is formally presented and applied to the description of the thermo-elastic response of the forsterite mineral.

Thermal Gradient Approach for the Quasi-harmonic Approximation and Its Application to Improved Treatment of Anisotropic Expansion

We present a novel approach to efficiently implement thermal expansion in the quasi-harmonic approximation (QHA) for both isotropic and more importantly, anisotropic expansion. In this approach, we rapidly determine a crystal's equilibrium volume and shape at a given temperature by integrating along the gradient of expansion from 0 Kelvin up to the desired temperature. We compare our approach to previous isotropic methods that rely on a brute-force grid search to determine the free energy minimum, which is infeasible to carry out for anisotropic expansion, as well as quasi-anisotropic approaches that take into account the contributions to anisotropic expansion from the lattice energy. We compare these methods for experimentally known polymorphs of piracetam and resorcinol and show that both isotropic methods agree to within error up to 300 K. Using the Grüneisen parameter causes up to 0.04 kcal/mol deviation in the Gibbs free energy, but for polymorph free energy differences there is a cancellation in error with all isotropic methods within 0.025 kcal/mol at 300 K. Anisotropic expansion allows the crystals to relax into lattice geometries 0.01-0.23 kcal/mol lower in energy at 300 K relative to isotropic expansion. For polymorph free energy differences all QHA methods produced results within 0.02 kcal/mol of each other for resorcinol and 0.12 kcal/mol for piracetam, the two molecules tested here, demonstrating a cancellation of error for isotropic methods. We also find that with expansion in more than a single volume variable, there is a non-negligible rate of failure of the basic approximations of QHA. Specifically, while expanding into new harmonic modes as the box vectors are increased, the system often falls into alternate, structurally distinct harmonic modes unrelated by continuous deformation from the original harmonic mode.

A quantum-mechanical investigation of oxygen vacancies and copper doping in the orthorhombic CaSnO3 perovskite

In this study we explore the implications of oxygen vacancy formation and of copper doping in the orthorhombic CaSnO3 perovskite, by means of density functional theory, focusing on energetic and electronic properties. In particular, the electronic charge distribution is analyzed by Mulliken, Hirshfeld-I, Bader and Wannier approaches. Calculations are performed at the PBE and the PBE0 level (for doping with Cu, only PBE0), with both spin-restricted and spin-unrestricted formulations; unrestricted calculations are used for spin-polarized cases and for the naturally open-shell cases (Cu doping). An oxygen vacancy is found to have the tendency to reduce Sn neighbors by giving rise to an energy band within the energy band-gap of the pristine system, close to the valence band. At variance with what happens in the CaTiO3 perovskite (also investigated here), an oxygen vacancy in the CaSnO3 perovskite is found to lose two valence electrons and thus to be positively charged so that no F-center is formed. Regarding Cu doping, when one Sn atom is substituted by a Cu one, the most stable configuration corresponds to having the Cu atom as a first neighbor to the vacancy. These findings shed some light on the catalytic and phosphorous host properties of this perovskite.

On the exfoliation and anisotropic thermal expansion of black phosphorus

Strong anisotropic thermal expansion of solid black phosphorus is predicted by means of accurate dispersion-corrected density functional theory calculations.

Intermolecular anharmonicity in molecular crystals: interplay between experimental low-frequency dynamics and quantum quasi-harmonic simulations of solid purine

A combined experimental spectroscopic and theoretical quasi-harmonic investigation of intermolecular anharmonicity in crystalline purine.

Thermal properties of molecular crystals through dispersion-corrected quasi-harmonic ab initio calculations: the case of urea

An ab initio quantum-mechanical theoretical framework is presented to compute the thermal properties of molecular crystals. The present strategy combines dispersion-corrected density-functional-theory (DFT-D), harmonic phonon dispersion, quasi-harmonic approximation to the lattice dynamics for thermal expansion and thermodynamic functions, and quasi-static approximation for anisotropic thermo-elasticity. The proposed scheme is shown to reliably describe thermal properties of the urea molecular crystal by a thorough comparison with experimental data.

Raman spectroscopic features of the neutral vacancy in diamond from ab initio quantum-mechanical calculations

Ab initio calculations of the Raman spectrum of the neutral vacancy in diamond reproduce observed spectral features of irradiated diamond up to the first-order peak.

Two-bit memory and quantized storage phenomenon in conventional MOS structures with double-stacked Pt-NCs in an HfAlO matrix

Two-bit memory and quantized storage phenomenon based on double-stacked Pt-NCs in an HfAlO matrix.

Anomalous mechanical strengths and shear deformation paths of Al2O3 polymorphs with high ionicity

Alumina (Al₂O₃) formed by selective oxidization provides an effective way to protect aluminide alloys against corrosion for sustainable applications.

Anharmonic thermal oscillations of the electron momentum distribution in lithium fluoride

Anharmonic thermal effects on the electron momentum distribution of a lithium fluoride single crystal are experimentally measured through high-resolution Compton scattering and theoretically modeled with ab initio simulations, beyond the harmonic approximation to the lattice potential, explicitly accounting for thermal expansion. Directional Compton profiles are measured at two different temperatures, 10 and 300 K, with a high momentum space resolution (0.10 a.u. in full width at half maximum), using synchrotron radiation. The effect of temperature on measured directional Compton profiles is clearly revealed by oscillations extending almost up to |p|=4  a.u., which perfectly match those predicted from quantum-mechanical simulations. The wave-function-based Hartree-Fock method and three classes of the Kohn-Sham density functional theory (local-density, generalized-gradient, and hybrid approximations) are adopted. The lattice thermal expansion, as described with the quasiharmonic approach, is found to entirely account for the effect of temperature on the electron momentum density within the experimental accuracy.