Interaction Energies Of Dimers Research Articles

Reproduction of experimental data for stacked caffeine dimers using various computational methods

Reliable description of stacking interaction of aromatic molecules is important for the understanding structure, stability, and functions of biopolymers. The caffeine molecule is an ideal object for this study as the stacking interactions are the preferential ones for self-associations of this hydrophobic molecule without H-bond donor groups. The analysis of anhydrous caffeine crystal structures revealed five types of caffeine stacking dimers. Geometry optimization of these dimers was performed using two molecular mechanics force fields, ab-initio method Møller Plesset of the second order (MP2), and density functional theory (DFT) with different functionals. The comparison of geometric parameters of the caffeine dimers obtained using different theoretical methods with those in crystals enables us to suggest the methods providing the most reliable stacking characteristics. These methods are: the MP2 with Basis Set Superposition Error correction (MP2/CP), Poltev force field, along with PBE0-DH, SCAN and PBE-D3 functionals of DFT. For the methods, which give the dimer interaction energy close to that obtained by MP2/CP method, the evaluated sublimation enthalpy values are shown to be close to the experimental data. Additionally, MP2/CP, Poltev FF and PBE0-DH functional showed to be the methods that describe well both the energy and geometry of the caffeine stacking dimer.

Improved modularity and new features in ipie: Toward even larger AFQMC calculations on CPUs and GPUs at zero and finite temperatures.

ipie is a Python-based auxiliary-field quantum Monte Carlo (AFQMC) package that has undergone substantial improvements since its initial release [Malone et al., J. Chem. Theory Comput. 19(1), 109-121 (2023)]. This paper outlines the improved modularity and new capabilities implemented in ipie. We highlight the ease of incorporating different trial and walker types and the seamless integration of ipie with external libraries. We enable distributed Hamiltonian simulations of large systems that otherwise would not fit on a single central processing unit node or graphics processing unit (GPU) card. This development enabled us to compute the interaction energy of a benzene dimer with 84 electrons and 1512 orbitals with multi-GPUs. Using CUDA and cupy for NVIDIA GPUs, ipie supports GPU-accelerated multi-slater determinant trial wavefunctions [Huang et al. arXiv:2406.08314 (2024)] to enable efficient and highly accurate simulations of large-scale systems. This allows for near-exact ground state energies of multi-reference clusters, [Cu2O2]2+ and [Fe2S2(SCH3)4]2-. We also describe implementations of free projection AFQMC, finite temperature AFQMC, AFQMC for electron-phonon systems, and automatic differentiation in AFQMC for calculating physical properties. These advancements position ipie as a leading platform for AFQMC research in quantum chemistry, facilitating more complex and ambitious computational method development and their applications.

Synthesis, QTAIM, anticancer activity analysis of pyrrole-imidazole/benzimidazole derivatives and investigation of their reactivity properties using DFT calculations and molecular docking

As part of our ongoing investigation into pyrrole derivatives, we here present the synthesis, spectroscopic characterization, QTAIM, reactivity, anticancer activity, and comparative experimental and computational analysis of pyrrole-imidazole ((3l), (3p)) and benzimidazole derivatives ((3h), (3i), (3j), (3k), (3m), (3n), (3o)). All synthesized compounds (3h-3p) have been well characterized by spectroscopic techniques (FT-IR, 1H and 13C NMR, Mass spectrometry). The experimental 1H and 13C NMR chemical shift values of synthesized pyrrole-imidazole (3l, 3p) and benzimidazole (3h-3o) derivatives have been well corroborated with computed chemical shifts. The vibrational analysis for four derivatives of pyrrole-benzimidazole (3m), (3n), (3o), and pyrrole-imidazole (3p) has the suitability for dimer formation in solid state by intermolecular heteronuclear hydrogen bonding (N–H···O) and the interaction energy of dimers are calculated to be 10.88, 11.70, 9.89 and 10.72 kcal/mol, using DFT. After basis-set superposition error (BSSE) correction, the interaction energies of dimers were found to be 11.12, 12.11, 10.13, and 11.52 kcal/mol. Estimated intermolecular H-bond in (3m-3n) compounds were found to be -13.38, -12.86, -11.02, and -11.28 kJ/mol using QTAIM. All the synthetic pyrrole-imidazole (3l, 3p) and benzimidazole (3h-3o) derivatives exhibit strong antileukemia activity in vitro against the proliferative cell line L1210 leukemia cells. A dataset of investigated compounds was subjected for molecular modelling simulation against three distinct proteins (SYK, PI3K, and BTK), which was found to be highly implicated in the favourable interaction between the compounds and their target proteins in every instance. The synthesized pyrrole-imidazole (3l, 3p) and benzimidazole (3h-3o) derivatives shown favourable interactions with their target proteins, with high activity and binding free energy values falling between 15.22 and 13.43 and -7.4 and -9.8 kcal/mol, respectively. The structure of pyrrole-imidazole (3l, 3p) and benzimidazole (3h-3o) derivatives is thoroughly examined, and several parameters are proposed here to improve their anticancer activity.

A Simple Model for the Pauli Repulsion with Possible Utility in QM, MM and Chemical Education.

The Pauli repulsion is the intermolecular force responsible for the volume and low compressibility of condensed-phase matter at normal conditions. A simple model for this force is presented, wherein per-atom electron densities are represented as spherical charge distributions that are prevented from significantly overlapping. In the example of two noble gas atoms approaching one another beyond their van der Waals radii, the distance between the centers of the electronic charge distributions becomes larger than the distance between the nuclei, giving rise to an unfavorable electrostatic interaction. For the purpose of calculating this interaction, the model is further simplified by representing the per-atom electron density as a negative point charge, loosely inspired by the classical Drude oscillator. The dispersion interaction is simplified to an R-6 term, centered on the aforementioned point charges. Despite the gross simplicity of the resulting formalism, near-quantitative agreement with high-level QM interaction energies of noble gas dimers is achieved. Accordingly, the present model is thought to have utility in force fields, in post-HF and post-DFT dispersion corrections, and in chemical education.

A polarizable valence electron density based force field for high-energy interactions between atoms and molecules.

High-accuracy molecular force field models suited for hot gases and plasmas are not as abundant as those geared toward ambient pressure and temperature conditions. Here, we present an improved version of our previous electron-density based force field model that can now account for polarization effects by adjusting the atomic valence electron contributions to match abinitio calculated Mulliken partial charges. Using a slightly modified version of the Hohenberg-Kohn theorem, we also include an improved theoretical formulation of our model when applied to systems with degenerate ground states. We present two variants of our polarizable model, fitted from abinitio reference data calculated at CCSD(T)/cc-pVTZ and CCSD(T)/CEP-31G levels of theory, that both accurately model water dimer interaction energies. Further improvements include the additional interaction components with fictitious non-spherically symmetric, yet atom-centered, electron densities and fitting the exchange and correlation coefficients against analytical expressions. The latter removes all unphysical oscillations that are observed in the previous non-polarizable variant of our force field.

Synonymous Mutations Can Alter Protein Dimerization Through Localized Interface Misfolding Involving Self-entanglements

Synonymous mutations in messenger RNAs (mRNAs) can reduce protein–protein binding substantially without changing the protein’s amino acid sequence. Here, we use coarse-grain simulations of protein synthesis, post-translational dynamics, and dimerization to understand how synonymous mutations can influence the dimerization of two E. coli homodimers, oligoribonuclease and ribonuclease T. We synthesize each protein from its wildtype, fastest- and slowest-translating synonymous mRNAs in silico and calculate the ensemble-averaged interaction energy between the resulting dimers. We find synonymous mutations alter oligoribonuclease’s dimer properties. Relative to wildtype, the dimer interaction energy becomes 4% and 10% stronger, respectively, when translated from its fastest- and slowest-translating mRNAs. Ribonuclease T dimerization, however, is insensitive to synonymous mutations. The structural and kinetic origin of these changes are misfolded states containing non-covalent lasso-entanglements, many of which structurally perturb the dimer interface, and whose probability of occurrence depends on translation speed. These entangled states are kinetic traps that persist for long time scales. Entanglements cause altered dimerization energies for oligoribonuclease, as there is a large association (odds ratio: 52) between the co-occurrence of non-native self-entanglements and weak-binding dimer conformations. Simulated at all-atom resolution, these entangled structures persist for long timescales, indicating the conclusions are independent of model resolution. Finally, we show that regions of the protein we predict to have changes in entanglement are also structurally perturbed during refolding, as detected by limited-proteolysis mass spectrometry. Thus, non-native changes in entanglement at dimer interfaces is a mechanism through which oligomer structure and stability can be altered.

Theoretical study on formation mechanism of acetic acid associating configurations and their distributions under saturated conditions.

The vapor-liquid equilibrium (VLE) properties of acetic acid systems generally behave strong non-ideality due to the associating interaction among acetic acid molecules. Theoretical study of the associating mechanism will provide guidance for the VLE property prediction, which is crucial for the designing on the separation process of the acetic acid systems. In this work, the association conformers and their distribution on acetic acid molecules in saturated gas and liquid phase were firstly studied. The proportions of the acetic acid monomer and multimers were obtained, which will contribute to the foundation for the vapor-liquid equilibrium simulations. The association mechanism on acetic acid molecules was then investigated by comparing among the structures and non-bonded interaction energies of different dimers. The structure of the cyclic dimer containing two OC-HO hydrogen bonds, may be found probably when acetic acid molecules approached. Electronic properties of different acetic acid dimers showed that the electrons around carbonyl oxygen atoms were deflected by the attraction of hydrogen atoms in the other molecule, which polarized the acetic acid molecules when the hydrogen bonds between acetic acid molecules were formed, providing theoretical basis for the polarized acetic acid molecular model. In this work, the molecular dynamics (MD) simulations and DFT calculations were conducted through the software GROMACS and Gaussian 09, respectively. For the MD simulations, the OPLS-AA force field was used as the atomic force field, with the cubic simulation cells constructed by Packmol program. For the DFT calculations, the M06-2X functional was employed for the optimization of the associating structures with the 6-311G** basis sets. Hydrogen bonding energies of dimers were corrected for the basis set superposition error (BSSE) and the deformation energies of monomers. Furthermore, the energy decomposition analysis was conducted at DFT/M06-2X/def-tzp level by the ADF software, and the wave function analysis was conducted by the Multiwfn software including the atom in molecule (AIM) topology analysis, the electronic potential analysis, and the electron density difference analysis.

NICE-FF: A non-empirical, intermolecular, consistent, and extensible force field for nucleic acids and beyond.

A new non-empirical abinitio intermolecular force field (NICE-FF in buffered 14-7 potential form) has been developed for nucleic acids and beyond based on the dimer interaction energies (IEs) calculated at the spin component scaled-MI-second order Møller-Plesset perturbation theory. A fully automatic framework has been implemented for this purpose, capable of generating well-polished computational grids, performing the necessary abinitio calculations, conducting machine learning (ML) assisted force field (FF) parametrization, and extending existing FF parameters by incorporating new atom types. For the ML-assisted parametrization of NICE-FF, interaction energies of ∼18 000 dimer geometries (with IE < 0) were used, and the best fit gave a mean square deviation of about 0.46 kcal/mol. During this parametrization, atom types apparent in four deoxyribonucleic acid (DNA) bases have been first trained using the generated DNA base datasets. Both uracil and hypoxanthine, which contain the same atom types found in DNA bases, have been considered as test molecules. Three new atom types have been added to the DNA atom types by using IE datasets of both pyrazinamide and 9-methylhypoxanthine. Finally, the last test molecule, theophylline, has been selected, which contains already-fitted atom-type parameters. The performance of NICE-FF has been investigated on the S22 dataset, and it has been found that NICE-FF outperforms the well-known FFs by generating the most consistent IEs with the high-level abinitio ones. Moreover, NICE-FF has been integrated into our in-house developed crystal structure prediction (CSP) tool [called FFCASP (Fast and Flexible CrystAl Structure Predictor)], aiming to find the experimental crystal structures of all considered molecules. CSPs, which were performed up to 4 formula units (Z), resulted in NICE-FF being able to locate almost all the known experimental crystal structures with sufficiently low RMSD20 values to provide good starting points for density functional theory optimizations.

Using Noncovalent Interactions to Test the Precision of Projector-Augmented Wave Data Sets.

The projector-augmented wave (PAW) method is one of the approaches that are widely used to approximately treat core electrons and thus to speed up plane-wave basis set electronic structure calculations. However, PAW involves approximations, and it is thus important to understand how they affect the results. Tests of the precision of PAW data sets often use the properties of isolated atoms or atomic solids. While this is sufficient to identify problematic PAW data sets, little information has been gained to understand the origins of the errors and suggest ways to correct them. Here, we show that the interaction energies of molecular dimers are very useful not only to identify problematic PAW data sets but also to uncover the origin of the errors. Using dimers from the S22 and S66 test sets and other dimers, we find that the error in the interaction energy is composed of a short-range component with an exponential decay and a long-range electrostatic part caused by an error in the total charge density. We propose and evaluate a simple improvable scheme to correct the long-range error and find that even in its simple and readily usable form, it is able to reduce the interaction energy errors to less than half on average for hydrogen-bonded dimers.

A quantitative assessment of deformation energy in intermolecular interactions: How important is it?

Dimer interaction energies have been well studied in computational chemistry, but they can offer an incomplete understanding of molecular binding depending on the system. In the current study, we present a dataset of focal-point coupled-cluster interaction and deformation energies (summing to binding energies, De) of 28 organic molecular dimers. We use these highly accurate energies to evaluate ten density functional approximations for their accuracy. The best performing method (with a double-ζ basis set), B97M-D3BJ, is then used to calculate the binding energies of 104 organic dimers, and we analyze the influence of the nature and strength of interaction on deformation energies. Deformation energies can be as large as 50% of the dimer interaction energy, especially when hydrogen bonding is present. In most cases, two or more hydrogen bonds present in a dimer correspond to an interaction energy of -10 to -25kcal mol-1, allowing a deformation energy above 1kcal mol-1 (and up to 9.5kcal mol-1). A lack of hydrogen bonding usually restricts the deformation energy to below 1kcal mol-1 due to the weaker interaction energy.

Unusual short intramolecular N–H⋅⋅⋅H–C contact and weak intermolecular interactions in two N-(adamantan-1-yl)piperazine carbothioamides: Crystallography, quantum chemical study and in vitro urease inhibitory activity

Crystal structures of two closely related N-(adamantan-1-yl)piperazine carbothioamides have been examined in detail using the Hirshfeld surface, fingerprint analysis, PIXEL energy for molecular dimers and noncovalent interaction (NCI) plots for intermolecular interactions. Both compounds namely, ethyl 4-[(adamantan-1-yl)carbamothioyl]piperazine-1-carboxylate (1) and N-(adamantan-1-yl)-4-(2-methoxyphenyl)piperazine-1-carbothioamide (2) crystallized in the triclinic system with two crystallographically independent molecules in each case. X-ray analysis indicates that the piperazine ring in one of the molecules of 1 exhibits a boat and chair conformation in the other crystallographically independent molecule, while the corresponding ring in 2 adopts a chair conformation. An analysis of the fingerprint plots of the Hirshfeld surface provides a qualitative picture of how carboxylate and methoxyphenyl substituents contribute to stabilizing the crystal packing. Both structures show unusually short intramolecular N–H⋅⋅⋅H–C contact with some geometrical constraints in addition to intramolecular C–H⋅⋅⋅S interactions. The role of intramolecular N–H⋅⋅⋅H–C contact was established with potential energy surface scan and structural optimization. The CLP-PIXEL calculation gives the intermolecular interaction energies for the molecular dimers in these structures. Many dimers in 1 are stabilized by C–H⋅⋅⋅O/S/π interactions, while others are stabilized by short H⋅⋅⋅H contacts. Intermolecular C–H⋅⋅⋅O interactions do not occur in 2. There are, however, intermolecular C–H⋅⋅⋅S/π interactions and short H⋅⋅⋅H contacts in some dimers. We used NCI plots to identify the nature of the observed noncovalent interactions. Compared to the control inhibitor (thiourea), the title compounds have good inhibitory activity against urease in vitro. Molecular docking analysis identifies the key active site residues involved in intermolecular interactions between a small molecule and an enzyme.

Asphaltene aggregation under the influence of structural features and interaction energies: Combination of quantum mechanical and molecular dynamics approaches

The importance of the model to predict the aggregation behavior of asphaltene molecules at the molecular level was well established in different studies. Elucidation of the relationship between the interaction energy and the structural characteristics of asphaltene molecules to their aggregation behavior still needs further investigation. For this purpose, we combined the quantum mechanics and molecular dynamics approaches and analyzed the interaction energy of asphaltene to find out the effect of structural features on the aggregation behavior. The interaction energy of asphaltene is used in this study to evaluate the potential of aggregation. We found that asphaltene molecules with smaller aromatic cores and shorter side chains form longer but more unstable stacks in the aggregation phase. If these structures do not have polar groups in the side chains, they will not show significant aggregation behavior in the clustering phase. Also, the length of stacks formed in the accumulation phase can be interpreted and predicted based on the terms such as attractive dispersion energy and steric repulsion in the interaction energy of asphaltene dimers. The aggregation process is explained by analyzing the nature of the interaction energy. As a result, by examining the effect of structural features on interaction energy, a relatively acceptable picture of the aggregation behavior of the asphaltene molecules can be obtained.

A Peptide Potential Based on a Bond Dipole Representation of Electrostatics

A potential based on a bond dipole representation of electrostatics is reported for peptides. Different from those popular force fields using atom-centered point-charge or point-multipole to express the electrostatics, our peptide potential uses the chemical bond dipole–dipole interactions to express the electrostatic interactions. The parameters for permanent and induced bond dipoles are derived from fitting to the MP2 three-body interaction energy curves. The parameters for van der Waals are taken from AMBER99sb and further refined from fitting to the MP2 stacking interaction energy curve. The parameters for bonded terms are taken from AMBER99sb without any modification. The scale factors for intramolecular dipole–dipole interactions are determined from reproducing the highly qualified ab initio conformational energies of dipeptides and tetrapeptides. The resulting potential is validated by use to evaluate the conformational energies of polypeptides containing up to 15 amino acid residues. The calculation results show that our peptide potential produces the conformational energies much closer to the famous density functional theory M06-2X/cc-pVTZ results than the famous AMBER99sb and AMOEBAbio18 force fields. Our potential also produces accurate intermolecular interaction energies for hydrogen-bonded and stacked dimers. We anticipate the peptide potential proposed here could be helpful in computer simulations of polypeptides and proteins.

Accurate Prediction of Three-Body Intermolecular Interactions via Electron Deformation Density-Based Machine Learning.

This work extends the electron deformation density-based descriptor, originally developed in the electron deformation density-based interaction energy machine learning (EDDIE-ML) algorithm to predict dimer interaction energies, to the prediction of three-body interactions in trimers. Using a sequential learning process to select the training data, the resulting Gaussian process regression (GPR) model predicts the three-body interaction energy within 0.2 kcal mol-1 of the SRS-MP2/cc-pVTZ reference values for the 3B69 and S22-3 trimer data sets. A hybrid kernel function is introduced, which combines contributions from the average and individual atomic environments, allowing the total trimer interaction energy to be predicted in addition to the three-body contribution using the same descriptor. To extend the range and diversity of trimer interaction energies available in the literature, a new data set based on a protein-ligand crystal structure is introduced, consisting of 509 structures of a central ligand with two protein fragments. Benchmark calculations are provided for the new data set, which contains significantly larger molecular interactions than current databases in the literature in addition to charged fragments. Compared to density funtional theory (DFT)- and wavefunction-based methods for calculating the three-body interaction energy, our model makes predictions in a significantly shorter time frame by reducing the number of required SCF calculations from 7 to 4 performed at the PBE0 level of theory, showcasing the utility and efficiency of our Δ-ML method particularly when applied to larger systems.

Benchmarking two-body contributions to crystal lattice energies and a range-dependent assessment of approximate methods.

Using the many-body expansion to predict crystal lattice energies (CLEs), a pleasantly parallel process, allows for flexibility in the choice of theoretical methods. Benchmark-level two-body contributions to CLEs of 23 molecular crystals have been computed using interaction energies of dimers with minimum inter-monomer separations (i.e., closest contact distances) up to 30 Å. In a search for ways to reduce the computational expense of calculating accurate CLEs, we have computed these two-body contributions with 15 different quantum chemical levels of theory and compared these energies to those computed with coupled-cluster in the complete basis set (CBS) limit. Interaction energies of the more distant dimers are easier to compute accurately and several of the methods tested are suitable as replacements for coupled-cluster through perturbative triples for all but the closest dimers. For our dataset, sub-kJ mol-1 accuracy can be obtained when calculating two-body interaction energies of dimers with separations shorter than 4 Å with coupled-cluster with single, double, and perturbative triple excitations/CBS and dimers with separations longer than 4 Å with MP2.5/aug-cc-pVDZ, among other schemes, reducing the number of dimers to be computed with coupled-cluster by as much as 98%.

Eutectic Mixture Formation and Relaxation Dynamics of Coamorphous Mixtures of Two Benzodiazepine Drugs

The formation of coamorphous mixtures of pharmaceuticals is an interesting strategy to improve the solubility and bioavailability of drugs, while at the same time enhancing the kinetic stability of the resulting binary glass and allowing the simultaneous administration of two active principles. In this contribution, we describe kinetically stable amorphous binary mixtures of two commercial active pharmaceutical ingredients, diazepam and nordazepam, of which the latter, besides being administered as a drug on its own, is also the main active metabolite of the other in the human body. We report the eutectic equilibrium-phase diagram of the binary mixture, which is found to be characterized by an experimental eutectic composition of 0.18 molar fraction of nordazepam, with a eutectic melting point of Te = 395.4 ± 1.2 K. The two compounds are barely miscible in the crystalline phase. The mechanically obtained mixtures were melted and supercooled to study the glass-transition and molecular-relaxation dynamics of amorphous mixtures at the corresponding concentration. The glass-transition temperature was always higher than room temperature and varied linearly with composition. The Te was lower than the onset of thermal decomposition of either compound (pure nordazepam decomposes upon melting and pure diazepam well above its melting point), thus implying that the eutectic liquid and glass can be obtained without any degradation of the drugs. The eutectic glass was kinetically stable against crystallization for at least a few months. The relaxation processes of the amorphous mixtures were studied by dielectric spectroscopy, which provided evidence for a single structural (α) relaxation, a single Johari-Goldstein (β) relaxation, and a ring-inversion conformational relaxation of the diazepinic ring, occurring on the same timescale in both drugs. We further characterized both the binary mixtures and pure compounds by FTIR spectroscopy and first-principles density functional theory (DFT) simulations to analyze intermolecular interactions. The DFT calculations confirm the presence of strong attractive forces within the heteromolecular dimer, leading to large dimer interaction energies of the order of -0.1 eV.

Protein-Ligand Binding Free-Energy Calculations with ARROW─A Purely First-Principles Parameterized Polarizable Force Field.

Protein-ligand binding free-energy calculations using molecular dynamics (MD) simulations have emerged as a powerful tool for in silico drug design. Here, we present results obtained with the ARROW force field (FF)─a multipolar polarizable and physics-based model with all parameters fitted entirely to high-level ab initio quantum mechanical (QM) calculations. ARROW has already proven its ability to determine solvation free energy of arbitrary neutral compounds with unprecedented accuracy. The ARROW FF parameterization is now extended to include coverage of all amino acids including charged groups, allowing molecular simulations of a series of protein-ligand systems and prediction of their relative binding free energies. We ensure adequate sampling by applying a novel technique that is based on coupling the Hamiltonian Replica exchange (HREX) with a conformation reservoir generated via potential softening and nonequilibrium MD. ARROW provides predictions with near chemical accuracy (mean absolute error of ∼0.5 kcal/mol) for two of the three protein systems studied here (MCL1 and Thrombin). The third protein system (CDK2) reveals the difficulty in accurately describing dimer interaction energies involving polar and charged species. Overall, for all of the three protein systems studied here, ARROW FF predicts relative binding free energies of ligands with a similar accuracy level as leading nonpolarizable force fields.

Non-covalent interactions towards 2-(4-(2,2-dicyanovinyl) benzylidene)malononitrile packing polymorphism due to solvent effect. Experimental and theoretical spectroscopy approach

Two polymorphs of 2-(4-(2,2-dicyanovinyl)benzylidene)malononitrile (I) were obtained by slow evaporation in acetone (Ia) and acetonitrile (Ib). These two polymorphic forms were analyzed by single-crystal XRD, which revealed both crystallized in the monoclinic crystal system and space group P21/n with Z = 2 (Z′= 0.5). Also, the SCXRD analysis evidenced that in the solvent-induced packing polymorphism; the Ia compound molecules are arranged in a slipped stacking pattern formed through the π···π interactions; while Ib molecules are arranged in a herringbone pattern stabilized by the intermolecular CH···N interactions. Packing polymorphism affects the fluorescence; for Ia crystals, the maximum emission wavelength was at 500 nm and for Ib was at 482 nm. The molecule structure features two C–C bonds with free rotation allowing conformational variation between polymorphs, and the principal difference is in molecular packing due to intramolecular and intermolecular interactions. The intermolecular interaction energies for the molecular dimers were obtained by the PIXEL method. The total lattice energy estimated using PIXELC module, was 32.71 and 34.03 kcalmol−1, for Ia and Ib, respectively; Ib showed a lower contribution of %Edis towards the total stabilization energy and might be due to a more significant number of stacking interactions formed in the crystal packing. Hirshfeld surface (HS) analysis and 2D-fingerprint plots were used to evaluate the relative contribution of non-covalent interactions (NCI) towards the crystal packing. The topology parameters suggested that the intermolecular interactions are weaker, and purely van der Waals and NCI plots were used to visualize the nature of non-covalent interactions. The complete assignments of all vibrational modes computed with potential energy distributions (PEDs) using the VEDA were in good agreement with experimental values; the difference is for the CN-stretching bands caused for the intramolecular interactions indicating possible charge transfer (CT). Natural bond orbital (NBO) analysis and electrostatic potential surfaces (MEPS) were performed to estimate the donor and acceptor sites in the molecule. Additionally, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and absorption wavelength were calculated by the time-dependent DFT approach. Using 1H and 13C chemical shifts to determine interactions before crystallization. The physicochemical characterization for both Ia and Ib did not show important differences using analytical techniques FT-IR, NMR, DSC/TGA, and PXRD.

Quantitative analysis of intermolecular interactions in crystalline substituted triazoles

This manuscript comprehensively examines four triazole derivatives using Hirshfeld surface and fingerprint analysis, PIXEL energy for molecular pairs, lattice energies for crystal packing, atoms-in-molecules (AIM) topological analysis, and noncovalent interaction (NCI) plots for intermolecular interactions. The fingerprint plots of the Hirshfeld surface analysis provide a quantitative picture of various substituent effects on the noncovalent interactions that contribute to the crystal packing stabilization of these four structures (TN1–TN4). The PIXEL method provides the intermolecular interaction energies for the molecular dimers observed in these structures. The nature and strength of intermolecular interactions at the (3, -1) bond critical point have been studied using the approach of atoms-in-molecules (AIM) via a topological analysis of the electron density distribution. The topology parameters suggested that the intermolecular interactions are classified as closed-shell interactions, and NCI plots were employed to identify the nature of the involved noncovalent interactions. Therefore, a detailed computational analysis renders insights into the electronic characteristics of different noncovalent interactions in the solid state of the structures in the current investigation.

Theoretical Study of the Structure and Binding Energies of Dimers of Zn(II)-Porphyrin Derivatives

Zinc-complexed porphyrin and chlorophyll derivatives form functional aggregates with remarkable photophysical and optoelectronic properties. Understanding the type and strength of intermolecular interactions between these molecules is essential for designing new materials with desired morphology and functionality. The dimer interactions of a molecular set composed of porphyrin derivatives obtained by substitutional changes starting from free-base porphyrin is studied. It is found that the B97M-rV/def2-TZVP level of theory provides a good compromise between the accuracy and cost to get the dimer geometries and interaction energies (IEs). The neglect of the relaxation energy due to the change in the monomer configurations upon complex formation causes a more significant error than the basis set superposition error. The metal complexation increases the binding energy by about −6 to −8 kcal/mol, and the introduction of keto and hydroxy groups further stabilizes the dimers by about −20 kcal/mol. Although the saturation of one of the pyrrol double bonds does not change the IE, the addition of R groups increases it.