Model Of Intermolecular Interactions Research Articles

Experimental in vivo models for understanding inter-molecular interactions and preventing multifactor disease development

The increased spontaneous fragility in the centromere regions of the chromosomes predisposes to abnormal cellular division due to abnormal interaction with the mitotic spindle, which leads to number chromosomal aberrations. The abnormal structure of the microtubule-associated proteins (MAPs) could also be among the internal factors, predisposing to these pathologies. On the other hand, the increased frequency of the spontaneous chromosomal fragility suggests abnormal structure of the respective chromosomal/chromatin components and thus an increased risk about gene mutations and structural chromosomal aberrations. The spontaneous chromosomal fragility was tested by light microscopy observation of metaphases from peripheral blood lymphocytes of 8 patients with polygene pathologies (neoplasms, neuro-degenerative diseases, and neuro-psychiatric disorders) and of 18 healthy controls. In the tested patients was established significantly higher frequency of the spontaneous chromosomal fragility, including in the centromere chromosomal regions, compared to the controls. Different inter-molecular interactions, which could prevent the pathology appearance, were investigated by appropriate experimental in vivo models. As a whole, in the most cases, the presented data showed significantly lower average titers of anti-ganglioside antibodies and gangliosides in the samples from myocardium and liver than in the samples from brain and pancreas. By taking into consideration that the myocardium and liver are known as the most enriched of GSH anatomic organs, the presented data could be explained with the literature messages of higher amounts of de novo-synthesized free GSH tri-peptide in the same two organs. Moreover, a possibility about the production of antibodies/immunoglobulins by non-lymphoid types of cells, tissues, and organs in appropriate conditions was shown. Because the so-produced antibodies are out of the germinative centers in the specialized lymphoid tissues and organs, the control of their functions by small ions and molecules as gangliosides is very important. In the current study, the attention was particularly directed to the iteractions with the participation of gangliosides, the reduced form of the tri-peptide glutathione (GSH), and the protein HACE1. Besides the tumor-suppressor activity of protein HACE1, also its neuroprotective influence was proven, namely by interactions with specific molecules.

Crystals of para-quaterphenyl and its trimethylsilyl derivative. I. Growth from solutions, structure and crystal chemical analysis by the Hirschfeld surface method

The results of crystal growth of para-quaterphenyl (4P) and its derivative – 4,4''-bis(trimethylsilyl)-para-quaterphenyl (TMS-4P-TMS) from solutions are presented. It has been established that TMS-4P-TMS crystals exhibit better growth characteristics compared to 4P. Parameters of phase transitions of 4P and TMS-4P-TMS in closed crucibles were refined using the method of differential scanning calorimetry. The crystal structure of TMS-4P-TMS in the triclinic space group P1 (Z = 2) has been decrypted for the first time using single-crystal X-ray diffraction and studied over a wide temperature range. Crystallographic analysis of the studied compounds in crystals was performed using the Hirshfeld surface method, and modeling of intermolecular interactions was conducted.

Integration of Wallach's Rule into Intermolecular Charge Transfer: A Visual Strategy for Chiral Purification.

Exploring the molecular packing and interaction between chiral molecules, no matter single enantiomer or racemates, is important for recognition and resolution of chiral drugs. However, sensitive and non-destructive analysis methods are lacking. Herein, an intermolecular-charge transfer (ICT) based spectroscopy is reported to reveal the differences in interaction between the achiral acceptor 1,2,4,5-tetracyanobenzene (TCNB) and the chiral donors, including S, R, and racemic naproxen (S/R/rac-NAP). In this process, S-NAP+TCNB and R-NAP+TCNB display a narrower band gap attributed to the newly formed ICT state. In contrast, the mixed rac-NAP and TCNB exhibit almost no significant change due to the strong affinity between the stereoisomers according to the Wallach's rule. Thus, S/R-NAP can be easily distinguished from rac-NAP based on significantly different optical behavior. The single crystal analysis, infrared spectroscopy, fluorescence spectroscopy, and theoretical calculation of naproxen confirm the importance of carboxyl for this differentiation in molecular packing and interaction. In addition, the esterification derivatization of naproxen achieves the manipulation of the intermolecular interaction model of racemates from the absolute Wallach's rule to a coexisting form of Wallach's rule and ICT. Further, visualized chiral purification of naproxen by the simple cocrystallization method is achieved through the collaboration of ICT and Wallach's rule.

Theoretical calculation of the parameters of the three-parameter chromatographic phase characterization method I. Dispersion forces parameter – generalized charge

In this work we studied the flavonoid composition of tangerine skins using 10 kinds of tangerines from the selectivity of separation in gas chromatography is determined by the nature of the stationary phase. The authors previously proposed a model of intermolecular interactions and a theoretical method of three-parameter characterisation of stationary phases in liquid chromatography based on it. They were applied to quantify the ability of molecules to participate in dispersion and dipole-dipole interactions and hydrogen bonds. The method proved to be efficient to describe the properties of stationary phases based on hydrocarbons, polyethylene glycol, polysiloxanes, and ionic liquids. The properties of stationary phases and analyte molecules are described by two selectivity characteristics: polarity and hydrophilicity, which can be calculated as a direct problem using the structural formula of the substance, or as an inverse problem using experimental data in the form of the Kovacs retention indices or Rohrschneider and McReynolds constants. No contradictions have been found between the characteristics calculated by the two methods. Using the proposed method, the relationship between the molecular weight of the polymer molecule and the values of selectivity characteristics was revealed. We proposed a selectivity map as a convenient and illustrative way to classify the stationary phases. Backed by the principle of similarity of properties, it can be used to determine the most selective stationary phase for a given analyte, without any experiments. The aim of this work was to determine the generalised charge as the first and key parameter of the three-parameter characterisation method. The main tool was the theory of generalised charges developed earlier in the laboratory of sorption methods of GEOKHI RAS. This theory, derived from fundamental principles, describes van der Waals interactions in the form of a Lennard-Jones potential, using the characteristics of molecules determined from their molecular structure. Previously, it successfully described nonpolar chromatographic systems. In the present study, we defined generalised charges, showed their relation to physical and experimental values, and provided calculation formulas for isolated molecules and for liquid phases. We presented the results of a detailed calculation of the generalised charges of substances of different classes, including gas chromatographic stationary phases.

On the intermolecular interactions and mechanical properties of polyvinyl alcohol/inositol supramolecular complexes

Hydrogen-bond (H-bond) cross-linking has recently been proven a promising strategy for simultaneously improving strength, toughness, and ductility of H-bonded polymers. However, there has been a lack of a fundamental understanding of how H-bond cross-linking works on a molecular level. To fill this knowledge gap, coarse-grained (CG) simulation provides a possibility because of its high computational efficiency and access to longer lengths and time scales. However, existing coarse-grained force fields and potential functions exhibit an inability to accurately describe H-bonded polymer systems. Herein, we report a modified CG model to understand the H-bond crosslinking effect of small molecules, inositol (IN) on polyvinyl alcohol (PVA), with reference to MARTINI 3.0 parameters and empirical data. The simulation results show that incorporating IN molecules results in a significant improvement in the strength, ductility, and toughness of PVA, which is in good agreement with experimental data. Moreover, the modified CG model establishes a close correlation between IN content, water content, tensile rate and glass transition, free volume, chain movement and mechanical properties of PVA. The results show that the yield strength of PVA initially increases and then decreases with the addition of IN. The maximum yield stress of PVA at IN-1.0 is approximately 155 MPa, representing a 33% increase compared to that of PVA. Additionally, the glass transition temperature (Tg) reaches 80.2 °C, ∼2.8 °C higher than that of pure PVA. This work develops a modified CG model for understanding intermolecular interactions and mechanical properties of H-bonded polymer systems on a molecular level. This understanding is expected to help expediate the material design and properties optimization of strong and tough polymeric materials.

Combining Force Fields and Neural Networks for an Accurate Representation of Bonded Interactions.

We present a formalism of a neural network encoding bonded interactions in molecules. This intramolecular encoding is consistent with the models of intermolecular interactions previously designed by this group. Variants of the encoding fed into a corresponding neural network may be used to economically improve the representation of torsional degrees of freedom in any force field. We test the accuracy of the reproduction of the ab initio potential energy surface on a set of conformations of two dipeptides, methyl-capped ALA and ASP, in several scenarios. The encoding, either alone or in conjunction with an analytical potential, improves agreement with ab initio energies that are on par with those of other neural network-based potentials. Using the encoding and neural nets in tandem with an analytical model places the agreements firmly within "chemical accuracy" of ±0.5 kcal/mol.

Edge-sharing water prisms.

Regular-shaped water clusters and nanostructures can be of particular interest for the self-assembly of complex structures and functional materials involving water molecules. Polyhedral water clusters are the most well studied. The low-energy structures of water hexamer, octamer and decamer are shaped like right prisms. The cavities of gas hydrates also have a polyhedral shape. Ice nanotubes are of no less interest both as configurations of global energy minima and in terms of possible applications. This article presents the results of the first systematic study of the structure and properties of a special class of water clusters. It reveals different combinations of three right prisms sharing an edge. According to modern calculations, the configurations of global energy minima of water clusters with the number of molecules being eighteen and twenty have this structure precisely. The topological characteristics of the edge-sharing water prisms are studied and the formulas for estimating the residual entropy are obtained. For these clusters (3-prisms), the usefulness of using a discrete model of intermolecular interaction [strong-weak-effective-bond model], previously developed for polyhedral water clusters, is shown. Calculations of the binding energy were performed using the non-additive Amoeba potential. To understand the relative stability of 3-prisms among other cluster forms, we use the structures recently reported in a published database containing over 3 × 106 unique water cluster networks (H2O)N of size N = 3-25 [Rakshit et al., J. Chem. Phys., 2019, 151(21), 214307, DOI: 10.1063/1.5128378].

Combining Force Fields and Neural Networks for an Accurate Representation of Chemically Diverse Molecular Interactions.

A key goal of molecular modeling is the accurate reproduction of the true quantum mechanical potential energy of arbitrary molecular ensembles with a tractable classical approximation. The challenges are that analytical expressions found in general purpose force fields struggle to faithfully represent the intermolecular quantum potential energy surface at close distances and in strong interaction regimes; that the more accurate neural network approximations do not capture crucial physics concepts, e.g., nonadditive inductive contributions and application of electric fields; and that the ultra-accurate narrowly targeted models have difficulty generalizing to the entire chemical space. We therefore designed a hybrid wide-coverage intermolecular interaction model consisting of an analytically polarizable force field combined with a short-range neural network correction for the total intermolecular interaction energy. Here, we describe the methodology and apply the model to accurately determine the properties of water, the free energy of solvation of neutral and charged molecules, and the binding free energy of ligands to proteins. The correction is subtyped for distinct chemical species to match the underlying force field, to segment and reduce the amount of quantum training data, and to increase accuracy and computational speed. For the systems considered, the hybrid ab initio parametrized Hamiltonian reproduces the two-body dimer quantum mechanics (QM) energies to within 0.03 kcal/mol and the nonadditive many-molecule contributions to within 2%. Simulations of molecular systems using this interaction model run at speeds of several nanoseconds per day.

Modulating Aggregation in Microemulsions: The Dispersion by Competitive Intermolecular Interaction Model.

A phenomenological model has been developed for the mechanism of action of phase modifiers as additives that control aggregation phenomena within water-in-oil emulsions. The "Dispersion by Competitive Intermolecular Interaction" model (DCI) explicitly considers the strength and prevalence of different intermolecular interactions that influence the molecular association of amphiphiles, the resulting distribution of aggregate size, and interaggregate interactions that influence phase phenomena. The existing "cosolvent" and "cosurfactant" association models, which describe the distribution of these amphiphiles within the solution, are re-examined in the context of intermolecular interactions. The different contributions of intermolecular interactions to the potential energy landscape of molecular association create distinct regimes within the DCI model that explain prior observations of cosolvent and cosurfactant behavior. The specific system under consideration, the N,N,N',N'-tetraoctyl diglycolamide amphiphile extractant with tributyl phosphate or dihexyl octanamide phase modifier additives, represents a new regime-labeled the polar disruption regime-where strong hydrogen bonding of the phase modifier with the polar-solutes disrupts the internal hydrogen bonding network of the polar micellar core, thereby decreasing aggregate size and narrowing the polydispersity in solution.

On a molecular origin of properties of water

Using the Reference-Average-Mayer perturbation theory, effective temperature-dependent site-site potentials are constructed from a realistic water model to provide a missing direct link between complex force fields (intermolecular interaction models) and artificial simple theoretical models used to explain properties of supercooled water. It is shown, using the TIP4P interaction model, that the effective site-site interactions change qualitatively their character with changes of thermodynamic conditions and assume, at low temperatures, the form of a double well which gives rise to the existence of two metastable forms of supercooled water. Since the theory possesses capacity to provide the site-site correlation functions even in an analytic form it may form a basis for developing a molecular-based equation of state of water.

Freeze-thaw and solvent-exchange strategy to generate physically cross-linked organogels and hydrogels of curdlan with tunable mechanical properties

Physical gels from natural polysaccharides present the advantage of no toxic cross-linking agents and no chemical modification during preparation. Herein, novel physical gels, transparent organogels and opaque hydrogels from the microorganism-derived (1,3)-β-D-glucan of curdlan were prepared in dimethyl sulfoxide (DMSO) using the freeze-thaw technique, followed by a solvent-exchange strategy with water. The mechanical and structural properties of these gels were investigated by rheology, scanning electron microscopy, attenuated total reflection infrared spectroscopy, wide-angle X-ray diffraction and small-angle X-ray scattering. Gelation mechanisms and intermolecular interaction models have also been proposed. The good solvent DMSO serves as both a crosslinker and a pore-foaming agent in organogels. The reversible macromolecular conformation changes and phase separation of curdlan endow the gels with reversible transparency, volume change and tunable mechanical strength. The new design strategy of facile preparation and performance tuning provides a platform for developing new organogels and sterile hydrogels of curdlan.

Molecular diffusion in gases and liquids

The diffusion coefficients in gases and liquids calculated by the molecular dynamics method with the use of the hard absolutely rough elastic spheres model are compared with those calculated using the Lennard-Jones potential. It is shown that dependences of reduced diffusion coefficients on density are similar, but differ numerically for different intermolecular interaction models. The simulation results have been compared with the experimental data on the diffusion in gaseous and liquid argon and in liquid benzene.

Efficacy of Chondroprotective Food Supplements Based on Collagen Hydrolysate and Compounds Isolated from Marine Organisms.

Osteoarthritis belongs to the most common joint diseases in humans and animals and shows increased incidence in older patients. The bioactivities of collagen hydrolysates, sulfated glucosamine and a special fatty acid enriched dog-food were tested in a dog patient study of 52 dogs as potential therapeutic treatment options in early osteoarthritis. Biophysical, biochemical, cell biological and molecular modeling methods support that these well-defined substances may act as effective nutraceuticals. Importantly, the applied collagen hydrolysates as well as sulfated glucosamine residues from marine organisms were strongly supported by both an animal model and molecular modeling of intermolecular interactions. Molecular modeling of predicted interaction dynamics was evaluated for the receptor proteins MMP-3 and ADAMTS-5. These proteins play a prominent role in the maintenance of cartilage health as well as innate and adapted immunity. Nutraceutical data were generated in a veterinary clinical study focusing on mobility and agility. Specifically, key clinical parameter (MMP-3 and TIMP-1) were obtained from blood probes of German shepherd dogs with early osteoarthritis symptoms fed with collagen hydrolysates. Collagen hydrolysate, a chondroprotective food supplement was examined by high resolution NMR experiments. Molecular modeling simulations were used to further characterize the interaction potency of collagen fragments and glucosamines with protein receptor structures. Potential beneficial effects of collagen hydrolysates, sulfated glycans (i.e., sulfated glucosamine from crabs and mussels) and lipids, especially, eicosapentaenoic acid (extracted from fish oil) on biochemical and physiological processes are discussed here in the context of human and veterinary medicine.

Formation of supramolecular synthons in the crystalline structure of the dinitrosyl iron complexes with aliphatic thiourea ligands.

By means of quantum-chemical calculations using Density Functional Theory, Quantum Theory of Atoms in Molecules, and Natural Bond Orbitals, theoretical modeling of intermolecular interactions has been performed for eight nitrosyl iron complexes with aliphatic thiourea ligands, which was aimed at discovering the presence of the NO…NO intermolecular interactions and at studying the possibility of the NO…NO supramolecular synthon formation in their crystalline structure for explaining their unusual magnetic properties. Such interactions were shown to be either stacking or T-like interactions, depending on the relative position of nitrosyl ligands and energetically corresponding to Van der Waals bonds. Mainly LP(O), π (NO), and π*(NO) orbitals in various combinations participate in their formation, with π (FeN), π(FeО), and LP(N) orbitals hardly being participants. The involvement of the NO bond orbitals results in quenching the orbital moment of the NO groups. If NO groups are isolated from intermolecular interactions, they can preserve the unquenched orbital moment.

Modulating the tension-time integral of the cardiac twitch prevents dilated cardiomyopathy in murine hearts.

Dilated cardiomyopathy (DCM) is often associated with sarcomere protein mutations that confer reduced myofilament tension–generating capacity. We demonstrated that cardiac twitch tension-time integrals can be targeted and tuned to prevent DCM remodeling in hearts with contractile dysfunction. We employed a transgenic murine model of DCM caused by the D230N-tropomyosin (Tm) mutation and designed a sarcomere-based intervention specifically targeting the twitch tension-time integral of D230N-Tm hearts using multiscale computational models of intramolecular and intermolecular interactions in the thin filament and cell-level contractile simulations. Our models predicted that increasing the calcium sensitivity of thin filament activation using the cardiac troponin C (cTnC) variant L48Q can sufficiently augment twitch tension-time integrals of D230N-Tm hearts. Indeed, cardiac muscle isolated from double-transgenic hearts expressing D230N-Tm and L48Q cTnC had increased calcium sensitivity of tension development and increased twitch tension-time integrals compared with preparations from hearts with D230N-Tm alone. Longitudinal echocardiographic measurements revealed that DTG hearts retained normal cardiac morphology and function, whereas D230N-Tm hearts developed progressive DCM. We present a computational and experimental framework for targeting molecular mechanisms governing the twitch tension of cardiomyopathic hearts to counteract putative mechanical drivers of adverse remodeling and open possibilities for tension-based treatments of genetic cardiomyopathies.

Atomic and ionic polarizabilities of B, C, N, O, and F

AbstractAccurate polarizabilities of atoms and molecules are critical in the treatment of optical and dielectric properties, in the modeling and interpretation of intermolecular interactions, in scattering processes, and in chemical reactivity. In this work we provide a systematic study of the atomic/ionic static dipole polarizabilities of the first‐row elements: B+, B, B−, C2+, C+, C, C−, N2+, N+, N, O2+, O+, O, O−, F2+, F+, F, and F−. We used the CCSD(T) method with a range of large correlation‐consistent basis sets augmented with a series of diffusion functions (x‐aug‐cc‐pVXZ). We discuss the trends in the dependence of dipole polarizability from the basis set size and/or number of diffuse functions and report the recommended values of average dipole polarizabilities for this series. The systematic survey of dipole polarizabilities for ions from boron to fluorine, including the extrapolation to complete basis set limit, is presented for the first time.

A MODEL OF INTERMOLECULAR INTERACTION ASSOCIATED WITH HYDROGEN BOND FORMATION AND ITS APPLICATION TO THE CHARACTERIZATION OF THE SELECTIVITY OF CHROMATOGRAPHIC PHASES ON THE EXAMPLE OF POLYETHYLENE GLYCOLS

The proposed model of intermolecular interactions contains three independent groups of quantities describing non-polar forces, polar forces, and hydrogen bonds. The contribution of hydrogen bonding to the total energy of intermolecular interaction is represented as a product of some quantum-mechanical threshold value and the probability of molecular arrangement that makes this bonding possible. Two characteristics, “polarity” and “hydrophilicity”, distinguishing polar and non-polar species, are introduced. Along with the generalized charge, these characteristics are independent arguments of the three-parameter model for liquid phases used in chromatography. The model is applied to describe the interaction of polar molecules in the gas phase with liquid polyethylenee glycol (PEG). Theoretical dependences of PEG polarity and hydrophilicity on the polymer′s molecular mass are derived. The graph of these dependences plotted in “polarity–hydrophilicity” coordinates agrees well chromatography data for characteristics of PEGs used as stationary phases.

On the role of intermolecular vibrational motions for ice polymorphs. II. Atomic vibrational amplitudes and localization of phonons in ordered and disordered ices.

We investigate the vibrational amplitudes and the degree of the phonon localization in 19 ice forms, both crystalline and amorphous, by a quasi-harmonic approximation with a reliable classical intermolecular interaction model for water. The amplitude in the low pressure ices increases with compression, while the opposite trend is observed in the medium and high pressure ices. The amplitude of the oxygen atom does not differ from that of hydrogen in low pressure ices apart from the contribution from the zero-point vibrations. This is accounted for by the coherent but opposite phase motions in the mixed translational and rotational vibrations. A decoupling of translation-dominant and rotation-dominant motions significantly reduces the vibrational amplitudes in any ice form. The amplitudes in ice III are found to be much larger than any other crystalline ice form. In order to investigate the vibrational mode characteristics, the moment ratio of the atomic displacements for individual phonon modes, called the inverse participation ratio, is calculated and the degree of the phonon localization in crystalline and amorphous ices is discussed. It is found that the phonon modes in the hydrogen-ordered ice forms are remarkably spread over the entire crystal having propagative or diffusive characteristic, while many localized modes appear at the edges of the vibrational bands, called dissipative modes, in the hydrogen-disordered counterparts. The degree of localization is little pronounced in low density amorphous and high density amorphous due to disordering of oxygen atoms.

Модель межмолекулярного взаимодействия с образованием водородной связи и ее применение для характеристики селективности хроматографических фаз на примере полиэтиленгликолей

Предложенная модель межмолекулярного взаимодействия содержит три независимые группы величин, описывающих неполярные, полярные силы и водородную связь, причем вклад водородной связи представлен как произведение пороговой величины, имеющей квантовую природу, на вероятность такого расположения молекул, при котором эта связь реализуется. Даны определения двух характеристик, отличающих полярные вещества от неполярных — «полярности» и «гидрофильности»; вместе с обобщенным зарядом эти характеристики являются независимыми аргументами трехпараметрической модели для жидких фаз, используемых в хроматографии. Модель применена для описания взаимодействия полярной молекулы газовой фазы с жидким полиэтиленгликолем (ПЭГ). Выводятся теоретические зависимости полярности и гидрофильности ПЭГ от молекулярной массы. График этих зависимостей, построенный в координатах «полярность—гидрофильность», хорошо согласуется с характеристиками ПЭГ как неподвижных фаз, полученными из хроматографических экспериментов.

Unstructured continuum–kinetic solver with fluid–particle interaction for in-space propulsion contaminant dispersal

A new parallel generalized unstructured grid solver for prediction of rarefied gas dynamics is presented. The method is based on the direct numerical solution of the semi-classical Boltzmann equation using a discrete velocity method (DVM) and supports accurate prediction of non-continuum flows in near-vacuum rarefied flow regimes. For in-space propulsion applications which involve mixed continuum–rarefied environments, the flow regimes are solved separately through the use of DVM and hybrid RANS/LES solution procedures, respectively, on the same computational domain while interacting with one another. The solver also supports coupled Lagrangian particle transport and coalescence/breakup modeling to enable prediction of plume flow impingement and contaminant dispersal through mixed continuum–rarefied environments around spacecraft. Such simulation capabilities are essential for the prediction of spacecraft environments concerning plume impingement pressure, heating, and contamination on spacecraft components such as solar panels and sensitive instruments. Example applications include venting and plume flow environments from spacecraft main engines and attitude control thrusters firing in near-vacuum conditions. The framework upon which the solvers are developed is introduced along with a detailed description of the direct Boltzmann solution and collision integral evaluation procedures. The accuracy of standalone kinetic and coupled continuum–kinetic predictions is validated by comparison against experimental data for shock structure using various different intermolecular interaction models. Results are presented to demonstrate the merits of the capability for prediction of high-speed gas–particle interaction through complex moving shock systems, and thruster plume flow impingement with liquid droplet tracking in near-vacuum conditions.