Martini 3 Coarse-Grained Force Field for Cholesterol

Cholesterol plays a crucial role in biomembranes by regulating various properties, such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the Martini model, Martini 3, offers significant improvements in interaction balance, molecular packing, and inclusion of new bead types and sizes. However, the release of the new model resulted in the need to reparameterize many core molecules, including cholesterol. Here, we describe the development and validation of a Martini 3 cholesterol model, addressing issues related to its bonded setup, shape, volume, and hydrophobicity. The proposed model mitigates some limitations of its Martini 2 predecessor while maintaining or improving the overall behavior.

An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation

Force fields (FFs) for molecular simulation have been under development for more than half a century. As with any predictive model, rigorous testing and comparisons of models critically depends on the availability of standardized data sets and benchmarks. While such benchmarks are rather common in the fields of quantum chemistry, this is not the case for empirical FFs. That is, few benchmarks are reused to evaluate FFs, and development teams rather use their own training and test sets. Here we present an overview of currently available tests and benchmarks for computational chemistry, focusing on organic compounds, including halogens and common ions, as FFs for these are the most common ones. We argue that many of the benchmark data sets from quantum chemistry can in fact be reused for evaluating FFs, but new gas phase data is still needed for compounds containing phosphorus and sulfur in different valence states. In addition, more nonequilibrium interaction energies and forces, as well as molecular properties such as electrostatic potentials around compounds, would be beneficial. For the condensed phases there is a large body of experimental data available, and tools to utilize these data in an automated fashion are under development. If FF developers, as well as researchers in artificial intelligence, would adopt a number of these data sets, it would become easier to compare the relative strengths and weaknesses of different models and to, eventually, restore the balance in the force.

Obtaining diffuse scattering patterns from computer simulations - a retrospective

The paper describes how the calculation of diffuse scattering from atomistic model crystals has developed over the last approximately 50 years. Not only has the quality of observed diffuse X-ray scattering data improved immensely with the advent of electronic area detectors and synchrotron radiation but the enormous increase in computer power has enabled patterns, of comparable quality to the observations, to be calculated from a Monte Carlo model.

Effect of solvent motions on the dynamics of the Diels-Alder reaction

How solvent motions affect the dynamics of chemical reactions in which the solute undergoes a substantial shape change is a fundamental but elusive issue. This work utilizes reactive simulation and Grote-Hynes theory to explore the effect of solvent motions on the dynamics of the Diels-Alder reaction (in the reverse direction, this reaction involves very substantial solute expansion) in aprotic solvents. The results reveal that the solvent environment is not sufficiently constraining to influence transition state passage dynamics, with the calculated transmission coefficients being close to unity. Even when solvent motions are suppressed or artificially slowed down, the solvent only affects the reaction dynamics in the transition state region to a very small extent. The only notable effect of solvent occurs far from the transition state region and corresponds to caging of the reactants within the reactant well.

Influence of Monovalent Salts on α-Glycine Crystal Growth from Aqueous Solution: Molecular Dynamics Simulations at Constant Supersaturation Conditions

The growth of α-glycine crystals from aqueous solution is investigated at constant supersaturations by utilizing the constant chemical potential molecular dynamics method. The study considers two faces (010) and (011) that predominantly determine the α-glycine crystal morphology. The general Amber force field (GAFF) with two different charge sets derived from semi-empirical calculations using the complete neglect of differential overlap method (CNDO) and from density functional calculations using the double-numerical plus d- and p-polarization basis set (DNP) is applied to describe α-glycine. The extended simple point charge model is used to simulate water. It is observed that the GAFF/DNP set leads to a much slower integration of glycine molecules into the crystal structure than the GAFF/CNDO set. The GAFF/CNDO set, however, causes the growth even at concentrations well below the experimental solubility. For the GAFF/DNP set, the influence of potassium chloride (KCl) and sodium chloride (NaCl) on the face growth rates is investigated. The parameters recently proposed by Yagasaki et al. [J. Chem. Theory Comput. 2020, 16, 2460-2473] are used to describe salt ions, as standard GAFF parameters lead to the unexpected formation of salt clusters at a concentration lower than the experimental solubility value. According to our simulation results, both salts suppress the growth of the (011) and (010) faces. The inhibiting effect of NaCl is much stronger than that of KCl for the (011) face, while both salts have a similar inhibiting effect on the (010) face. The results are in line with the experimental observations of the impact of salt ions on the α-glycine growth rates for the (011) face reported in literature.

Eshelby untwisting

The concept of Eshelby untwisting, the effect of an axial screw dislocation driving an intrinsically twisted nanocrystal towards a straighter configuration more consistent with long-range translational symmetry, is introduced here. Force-field simulations of nanorods built from the enantiomorphous (space groups, P3₁21 and P3₂21) crystal structures of benzil (C₆H₅-C(O)-C(O)-C₆H₅) were previously shown to twist in opposite directions, even in the absence of dislocations. Here, both right- and left-handed screw dislocations were introduced into benzil nanorods in silico. For rods built from the P3₂21 enantiomorph, dislocations with negative Burgers vectors increased the right-handed twisting already present in the intrinsically twisted structures without dislocations, whereas dislocations with positive Burgers vectors drove the twisted structure back towards a straight configuration, untwisting. In the dynamic simulations, the P3₂21 helicoid endowed with a positive Burgers vector ultimately twisted back through the straight configuration, until a helicoid of opposite sense from that of the starting structure, was obtained. The bearing of these observations on the propensity of small crystals to adopt non-polyhedral morphologies is discussed.

In situ nanoscale visualization of solvent effects on molecular crystal surfaces

Atomic force microscopy and molecular dynamics simulations probed the crystallinity and hydrophobicity of a paracetamol crystal surface in water–ethanol mixtures. We observe the formation of a dynamic heterogenous disordered surface (DHDS) layer.

Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

Molecular dynamics (MD) simulations have become increasingly useful in the modern drug development process. In this review, we give a broad overview of the current application possibilities of MD in drug discovery and pharmaceutical development. Starting from the target validation step of the drug development process, we give several examples of how MD studies can give important insights into the dynamics and function of identified drug targets such as sirtuins, RAS proteins, or intrinsically disordered proteins. The role of MD in antibody design is also reviewed. In the lead discovery and lead optimization phases, MD facilitates the evaluation of the binding energetics and kinetics of the ligand-receptor interactions, therefore guiding the choice of the best candidate molecules for further development. The importance of considering the biological lipid bilayer environment in the MD simulations of membrane proteins is also discussed, using G-protein coupled receptors and ion channels as well as the drug-metabolizing cytochrome P450 enzymes as relevant examples. Lastly, we discuss the emerging role of MD simulations in facilitating the pharmaceutical formulation development of drugs and candidate drugs. Specifically, we look at how MD can be used in studying the crystalline and amorphous solids, the stability of amorphous drug or drug-polymer formulations, and drug solubility. Moreover, since nanoparticle drug formulations are of great interest in the field of drug delivery research, different applications of nano-particle simulations are also briefly summarized using multiple recent studies as examples. In the future, the role of MD simulations in facilitating the drug development process is likely to grow substantially with the increasing computer power and advancements in the development of force fields and enhanced MD methodologies.

Potential energy function for a photo-switchable lipid molecule

Photo-switchable lipids are synthetic lipid molecules used in photo-pharmacology to alter membrane lateral pressure and thus control opening and closing of mechanosensitive ion channels. The molecular picture of how photo-switchable lipids interact with membranes or ion channels is poorly understood. To facilitate all-atom simulations that could provide a molecular picture of membranes with photo-switchable lipids, we derived force field parameters for atomistic computations of the azobenzene-based fatty acid FAAzo-4. We implemented a Phyton-based algorithm to make the optimization of atomic partial charges more efficient. Overall, the parameters we derived give good description of the equilibrium structure, torsional properties, and non-bonded interactions for the photo-switchable lipid in its trans and cis intermediate states, and crystal lattice parameters for trans-FAAzo-4. These parameters can be extended to all-atom descriptions of various photo-switchable lipids that have an azobenzene moiety.

A Short Review of Current Computational Concepts for High-Pressure Phase Transition Studies in Molecular Crystals

High-pressure chemistry of organic compounds is a hot topic of modern chemistry. In this work, basic computational concepts for high-pressure phase transition studies in molecular crystals are described, showing their advantages and disadvantages. The interconnection of experimental and computational methods is highlighted, showing the importance of energy calculations in this field. Based on our deep understanding of methods’ limitations, we suggested the most convenient scheme for the computational study of high-pressure crystal structure changes. Finally, challenges and possible ways for progress in high-pressure phase transitions research of organic compounds are briefly discussed.

Molecular dynamics simulation of organic crystals: introducing the CLP-dyncry environment

The CLP-dyncry molecular dynamics (MD) program suite and force field environment is introduced and validated with its ad hoc features for the treatment of organic crystalline matter. The package, stemming from a preliminary implementation on organic liquids (Gavezzotti & Lo Presti, 2019), includes modules for the preliminary generation of molecular force field files from ab initio derived force constants, and for the preparation of crystalline simulation boxes from general crystallographic information, including Cambridge Structural Database CIFs. The intermolecular potential is the atom–atom Coulomb–London–Pauli force field, well tested as calibrated on sublimation enthalpies of organic crystals. These products are then submitted to a main MD module that drives the time integration and produces dynamic information in the form of coordinate and energy trajectories, which are in turn processed by several kinds of crystal-oriented analytic modules. The whole setup is tested on a variety of bulk crystals of rigid, non-rigid and hydrogen-bonded compounds for the reproduction of radial distribution functions and of crystal-specific collective orientational variables against X-ray data. In a series of parallel tests, some advantages of a dedicated program as opposed to software more oriented to biomolecular simulation (Gromacs) are highlighted. The different and improved view of crystal packing that results from joining static structural information from X-ray analysis with dynamic upgrades is also pointed out. The package is available for free distribution with I/O examples and Fortran source codes.

Stepwise Homogeneous Melting of Benzene Phase I at High Pressure

We investigate, using molecular dynamics simulations, the spontaneous homogeneous melting of benzene phase I under a high pressure of 1.0 GPa. We find an apparent stepwise transition via a metastable crystal phase, unlike the direct melting observed at ambient pressure. The transition to the metastable phase is achieved by rotational motions, without the diffusion of the center of mass of benzene. The metastable crystal completely occupies the whole space and maintains its structure for at least several picoseconds, so that the phase seems to have a local free energy minimum. The unit cell is found to be unique—no such crystalline structure has been reported so far. Furthermore, we discuss the influence of pressure control on the melting behavior.

Effects of Solvent Stabilization on Pharmaceutical Crystallization: Investigating Conformational Polymorphism of Probucol Using Combined Solid-State Density Functional Theory, Molecular Dynamics, and Terahertz Spectroscopy

Solid-state density functional theory (DFT), molecular dynamics (MD), and terahertz (THz) spectroscopy were used to study the formation of enantiotropically related conformational Form I and Form II polymorphs of the pharmaceutical compound, probucol. DFT calculations were performed on the crystal systems to compare relative lattice energies and the solvent stabilization of the metastable Form II structure. The thermodynamics of solvent inclusion in the Form II·MeOH crystal system were determined from MD simulations, as was the favored conformation of molecular probucol in methanol and ethanol solutions. The findings from both solid-state DFT and MD calculations suggest that the preferred molecular orientations of the probucol molecule in solution and the probable inclusion of methanol in the crystal lattice during the crystallization process lead to the solvent selectivity of the probucol polymorph formation. The additional stabilization energy provided by the crystallization solvent facilitates the nucleation and growth of the Form II polymorph under conditions that favor this metastable crystal form over the thermodynamically stable Form I, despite the higher energy molecular and crystalline configurations of probucol Form II. We demonstrate the influence of solvent on the formation of pharmaceutical polymorphs and provide a molecular-level view of complex interactions leading to polymorphism using a combination of computational methods and THz spectral data.

Computational Study on Homogeneous Melting of Benzene Phase I

Molecular-dynamics simulations are used for examining the microscopic details of the homogeneous melting of benzene phase I. The equilibrium melting temperatures of our model were initially determined using the direct-coexistence method. Homogeneous melting at a higher temperature is achieved by heating a defect- and surfacefree crystal. The temperature-dependent potential energy and lattice parameters do not indicate a premelting phase even under superheated conditions. Further, statistical analyses using induction times computed from 200 melting trajectories were conducted, denoting that the homogeneous melting of benzene occurs stochastically, and that there is no intermediate transient state between the crystal and liquid phases. Additionally, the critical nucleus size is estimated using the seeding approach, along with the local bond order parameter. We found that the large diffusive motion arising from defect migration or neighbor-molecule swapping is of little importance during nucleation. Instead, the orientational disorder activated using the flipping motion of the benzene plane results in the melting nucleus.

Impact of morphology, side-chains, and crystallinity on charge-transport properties of π-extended double helicenes

We report a computational study on the effect of side-chain substitution, heteroaromatic substitution and unique crystal packing on the charge transport and mobility of three double helicene molecules. These double helicene (DH) molecules, having curved π-conjugation, are structural hybrids of non-planar [6]helicene and planar tribenzo[b,n,pqr]perylene (TBP). We find that side-chain substitution has only a effect on intrinsic electronic properties in DHs but dramatically impacts the packing arrangement, morphologies and transport network, exhibited in calculated charge transport parameters. Interestingly, the dimensionality of the transport evolves from one dimensional to three dimensional with side-chain substitution (DH2) and heteroaromatic substitution (DH3). Using two different well-known transport models, we have established a direct link between the morphology, transport connectivity, and hole mobilities. While both unsubstituted and substituted DHs exhibit high hole mobilities in the ordered phase, the results show that with inclusion of positional disorder, the mobilities of disordered DH1 and DH3 are lower while the mobility of DH2 remain nearly unchanged. We relate this effect to the dimensionality of their unique transport networks. These DH molecules are promising organic semiconductors with high mobilities in ordered and disordered phases, with predicted values that lie in the range of ∼1 to 10 cm2 V-1 s-1.

A jumping crystal predicted with molecular dynamics and analysed with TLS refinement against powder diffraction data

By running a temperature series of molecular dynamics (MD) simulations starting from the known low-temperature phase, the experimentally observed phase transition in a 'jumping crystal' was captured, thereby providing a prediction of the unknown crystal structure of the high-temperature phase and clarifying the phase-transition mechanism. The phase transition is accompanied by a discontinuity in two of the unit-cell parameters. The structure of the high-temperature phase is very similar to that of the low-temperature phase. The anisotropic displacement parameters calculated from the MD simulations readily identified libration as the driving force behind the phase transition. Both the predicted crystal structure and the phase-transition mechanism were verified experimentally using TLS (translation, libration, screw) refinement against X-ray powder diffraction data.

Determining short-lived solid forms during phase transformations using molecular dynamics

We demonstrate that elusive high-energy metastable crystal structures can be determined from molecular dynamics simulations.

The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine

Motional averaging has been proven to be significant in predicting the chemical shifts in ab initio solid-state NMR calculations, and the applicability of motional averaging with molecular dynamics has been shown to depend on the accuracy of the molecular mechanical force field. The performance of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base cocaine is used as an example. The results reveal that, even though the TMFF outperforms the COMPASS force field for representing the energies and conformations of predicted structures, it does not give significant improvement in the accuracy of NMR calculations. Further studies should direct more attention to anisotropic chemical shifts and development of the method of solid-state NMR calculations.

Controlling Thermal Expansion: A Metal-Organic Frameworks Route

Controlling thermal expansion is an important, not yet resolved, and challenging problem in materials research. A conceptual design is introduced here, for the first time, for the use of metal-organic frameworks (MOFs) as platforms for controlling thermal expansion devices that can operate in the negative, zero, and positive expansion regimes. A detailed computer simulation study, based on molecular dynamics, is presented to support the targeted application. MOF-5 has been selected as model material, along with three molecules of similar size and known differences in terms of the nature of host-guest interactions. It has been shown that adsorbate molecules can control, in a colligative way, the thermal expansion of the solid, so that changing the adsorbate molecules induces the solid to display positive, zero, or negative thermal expansion. We analyze in depth the distortion mechanisms, beyond the ligand metal junction, to cover the ligand distortions, and the energetic and entropic effect on the thermo-structural behavior. We provide an unprecedented atomistic insight on the effect of adsorbates on the thermal expansion of MOFs as a basic tool toward controlling the thermal expansion.

Computational Dehydration of Crystalline Hydrates Using Molecular Dynamics Simulations

Molecular dynamics (MD) simulations have evolved to an increasingly reliable and accessible technique and are today implemented in many areas of biomedical sciences. We present a generally applicable method to study dehydration of hydrates based on MD simulations and apply this approach to the dehydration of ampicillin trihydrate. The crystallographic unit cell of the trihydrate is used to construct the simulation cell containing 216 ampicillin and 648 water molecules. This system is dehydrated by removing water molecules during a 2200 ps simulation, and depending on the computational dehydration rate, different dehydrated structures were observed. Removing all water molecules immediately and removing water relatively fast (10 water molecules/10 ps) resulted in an amorphous system, whereas relatively slow computational dehydration (3 water molecules/10 ps) resulted in a crystalline anhydrate. The structural changes could be followed in real time, and in addition, an intermediate amorphous phase was identified. The computationally identified dehydrated structure (anhydrate) was slightly different from the experimentally known anhydrate structure suggesting that the simulated computational structure could represent a kinetically trapped dehydration intermediate.

Force-field parameters for beryllium complexes in amorphous layers

Unknown force-field parameters for metal organic beryllium complexes used in emitting and electron transporting layers of OLED structures are determined. These parameters can be used for the predictive atomistic simulations of the structure and properties of amorphous organic layers containing beryllium complexes. The parameters are found for the AMBER force field using a relaxed scan procedure and quantum-mechanical DFT calculations of potential energy curves for specific internal (angular) coordinates in a series of three Be complexes (Bebq2; Be(4-mpp)2; Bepp2). The obtained parameters are verified in calculations of some molecular and crystal structures available from either quantum-mechanical DFT calculations or experimental data. Graphical Abstract Beryllium complexes in amorphous layersᅟ.

Crystallographic and Dynamic Aspects of Solid-State NMR Calibration Compounds: Towards ab Initio NMR Crystallography

The excellent results of dispersion-corrected density functional theory (DFT-D) calculations for static systems have been well established over the past decade. The introduction of dynamics into DFT-D calculations is a target, especially for the field of molecular NMR crystallography. Four (13) C ss-NMR calibration compounds are investigated by single-crystal X-ray diffraction, molecular dynamics and DFT-D calculations. The crystal structure of 3-methylglutaric acid is reported. The rotator phases of adamantane and hexamethylbenzene at room temperature are successfully reproduced in the molecular dynamics simulations. The calculated (13) C chemical shifts of these compounds are in excellent agreement with experiment, with a root-mean-square deviation of 2.0 ppm. It is confirmed that a combination of classical molecular dynamics and DFT-D chemical shift calculation improves the accuracy of calculated chemical shifts.

Dynamic quantum crystallography: lattice-dynamical models refined against diffraction data. I. Theory

This study demonstrates and tests the refinement of a lattice-dynamical model derived from periodic ab initio calculations at the Γ point against elastic diffraction data (X-ray or neutron). Refinement of only a handful of parameters is sufficient to obtain a similar agreement with the data as the conventional crystallographic model using anisotropic displacement parameters. By refinement against X-ray data, H displacement parameters are obtained which compare favourably with those from neutron diffraction experiments. The approach opens the door for evaluating thermodynamic properties, and for refinement against multi-temperature data, against inelastic diffraction data, spectroscopic information and thermal diffuse scattering data.

On the use of molecular dynamics simulation to calculate X-ray thermal diffuse scattering from molecular crystals

The use of molecular dynamics simulations to calculate the thermal diffuse scattering from X-ray diffraction experiments on molecular crystals is described, using the crystal structure of aspirin form I as an example system. Parameter settings that do not affect the actual simulation are varied in order to examine the effect on the final calculated diffraction pattern, and thus roughly determine a range for general settings that might be used in further experiments targeted at tailoring parameters associated with the functional forms for dispersion interaction terms commonly used in molecular simulation force fields. The proposed method is compared with that of the more widely accepted Monte Carlo technique, and possible advantages and drawbacks for the use of either method are discussed.

Do solid-to-solid polymorphic transitions in DL-norleucine proceed through nucleation?

DL-Norleucine is a molecular crystal exhibiting two enantiotropic phase transitions. The high temperature α ↔ γ transition has been shown to proceed through nucleation and growth [Mnyukh et al., J. Phys. Chem. Solids, 1975, 36, 127]. We focus on the low temperature β ↔ α transition in a combined computational and experimental study. The temperature dependence of the structural and energetic properties of both polymorphic forms is nearly identical. Molecular dynamics simulations and nudged elastic band calculations of the transition process itself, suggest that the transition is governed by cooperative movements of bilayers over relatively large energy barriers.

QM/MM investigations of organic chemistry oriented questions

About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.

Simulations of guest transport in clathrates of Dianin's compound and hydroquinone

Clathrates have been proposed for use in a variety of applications including gas storage, mixture separation and catalysis due to the potential for controlled guest diffusion through their porous lattices. Here molecular dynamics simulations are employed to study guest transport in clathrates of hydroquinone (HQ) and Dianin's compound (DC). Systems investigated were HQ with methanol and acetonitrile, and DC with methanol and ethanol. Simulations were set up with one guest in the pore, two guests in the pore and one vacancy in the pore and a filled pore, and free-energy barriers for movement between cavities of the pore were estimated for all cases. Comparison between these simulations indicates that guest transport most likely proceeds by molecules moving from full to empty cavities consecutively, one by one, rather than in a concerted manner. Thus, the presence of empty cavities is very important for guest transport, which becomes more energetically demanding in fully loaded systems. Flexibility of the host can assist guest transport. In the studied DC clathrates transport occurs via an intermediate conformation in which the hydroxyl group of the alcohol guest molecule participates in the hydrogen-bonded ring of the host. We also address the issue of the number of methanol guest molecules that DC accommodates, for which conflicting information exists. We found that this is likely to be temperature dependent and suggest that under some conditions the system is most likely non-stoichiometric.

Computational studies of crystal structure and bonding

The analysis, prediction, and control of crystal structures are frontier topics in present-day research in view of their importance for materials science, pharmaceutical sciences, and many other chemical processes. Computational crystallography is nowadays a branch of the chemical and physicals sciences dealing with the study of inner structure, intermolecular bonding, and cohesive energies in crystals. This chapter, mainly focused on organic compounds, first reviews the current methods for X-ray diffraction data treatment, and the new tools available both for quantitative statistical analysis of geometries of intermolecular contacts using crystallographic databases and for the comparison of crystal structures to detect similarities or differences. Quantum chemical methods for the evaluation of intermolecular energies are then reviewed in detail: atoms-in-molecules and other density-based methods, ab initio MO theory, perturbation theory methods, dispersion-supplemented DFT, semiempirical methods and, finally, entirely empirical atom-atom force fields. The superiority of analyses based on energy over analyses based on geometry is highlighted, with caveats on improvised definitions of some intermolecular chemical bonds that are in fact no more than fluxional approach preferences. A perspective is also given on the present status of computational methods for the prediction of crystal structures: in spite of great steps forward, some fundamental obstacles related to the kinetic-thermodynamic dilemma persist. Molecular dynamics and Monte Carlo methods for the simulation of crystal structures and of phase transitions are reviewed. These methods are still at a very speculative stage, but hold promise for substantial future developments.