Interactions In Molecular Systems Research Articles

HBCalculator: A Tool for Hydrogen Bond Distribution Calculations in Molecular Dynamics Simulations.

Hydrogen bonds, crucial noncovalent interactions in molecular systems, significantly impact biological, chemical, and energy-related processes; therefore, characterizing hydrogen bond information is of importance to fundamental studies. This work introduces the HBCalculator, a Tcl-based tool integrated with VMD for calculating 1D and 2D distributions of hydrogen bond density and strength. The tool facilitates spatial analysis, overcoming limitations in existing packages that lack direct spatial distribution output. By employing HBCalculator in MD simulations, three systems of cellulose/water and graphene/water interfaces, were tested to showcase its functionality. The 1D and 2D hydrogen bond distributions reveal insights into interfacial properties, reflecting the impact of material hydrophobicity. The simplicity of usage, along with its potential for diverse molecular systems, positions HBCalculator as a valuable tool for researchers exploring hydrogen bond networks.

Reparameterization of Polarizable Force Fields for Studying Ion Transfer across Liquid-Liquid Interfaces.

We have developed a general scheme for refining classical polarizable molecular dynamics (MD) force fields that can accurately describe the molecular interactions in systems with liquid-liquid interfaces. While ab initio MD (AIMD) simulations can naturally describe molecular interactions, they are often so computationally expensive that simulating large system sizes and/or long time scales is usually infeasible. To resolve this, we parameterized efficient and accurate classical polarizable force fields that use AIMD reference data by minimizing both the relative entropy and the root mean squared deviation in atomic forces. We utilized our new multiscale models to study chloride ion transfer across the water-dichloromethane (DCM) interface with and without the tetraethylammonium cation as the phase-transfer catalyst. Our calculated free-energy barrier for the water-DCM interface is consistent with the other reported simulation results. We further analyzed the ion-transfer process by studying the hydration shell structures around the chloride ion and the ion-pair formation to better understand the mechanism. We observed that electronic polarizability is an important factor for the studied phase-transfer catalyst to lower the free-energy barrier of the ion transfer. Using the water-benzene interface system as an additional example, we show that our parameterization scheme provides a general route for modeling different liquid-liquid interface systems even when the experimental data or force field parameters are not readily available.

A cutoff-based method with charge-distribution-data driven pair potentials for efficiently estimating electrostatic interactions in molecular systems.

We introduce a simple cutoff-based method for precise electrostatic energy calculations in the molecular dynamics (MD) simulations of point-particle systems. Our method employs a theoretically derived smooth pair potential function to define electrostatic energy, offering stability and computational efficiency in MD simulations. Instead of imposing specific physical conditions, such as dielectric environments or charge neutrality, we focus on the relationship represented by a single summation formula of charge-weighted pair potentials. This approach allows an accurate energy approximation for each particle, enabling a straightforward error analysis. The resulting particle-dependent pair potential captures the charge distribution information, making it suitable for heterogeneous systems and ensuring an enhanced accuracy through distant information inclusion. Numerical investigations of the Madelung constants of crystalline systems validate the method's accuracy.

Methyl orange-doped thiourea barium chloride crystals: Natural bond orbital analysis of the fock matrix for laser applications

Pure thiourea barium chloride (TBC) crystals were synthesised using a slow cooling rate (0.05°C/day) and gradual evaporation from an aqueous solution. The growth process occurred over more than 19 days at a temperature of 39°C. Natural bond orbital (NBO) analysis has proven beneficial for studying charge transfer and conjugative interactions in molecular systems. Moreover, it sheds light on intermolecular bonding, and the interactions between these bonds have implications for optical applications. Additionally, the charge transfer interactions within the molecule that influence its catalytic activity can be elucidated by a lower HOMO and LUMO energy gap. This energy difference can be an indicator of a compound’s excitability; the more readily a compound can be excited, the narrower the energy gap. The energy gap might be significantly affected by the influence of thermal energy. The non-linear optical (NLO) efficiency of methyl orange-doped (MOD) TBC crystals was contrasted with that of the pure form, and the doped version exhibited greater efficiency, particularly for high-frequency applications.

Molecular Electrostatic Potential Topology Analysis of Noncovalent Interactions.

ConspectusThe topology of molecular electrostatic potential (MESP), V(r), derived from a reliable quantum chemical method has been used as a powerful tool for the study of intermolecular noncovalent interactions. The MESP topology mapping is achieved by computing both ∇V(r) data and the elements of the Hessian matrix at ∇V(r) = 0, the critical point. MESP minimum (Vmin) as well as MESP at a reaction center, specific to an atom (Vn), have been employed as electronic parameters to interpret the variations in the reactivity (activation/deactivation) of chemical systems with respect to the influence of substituents, ligands, π-conjugation, aromaticity, trans influence, hybridization effects, steric effects, cooperativity, noncovalent interactions, etc. In this Account, several studies involving MESP topology analysis, which yielded interpretations of various noncovalent interactions and also provided new insights in the area of chemical bonding, are highlighted. The existence of lone pairs in molecules is distinctly reflected by the topology features of the MESP minima (Vmin). The Vmin is able to probe lone pairs in molecules, and it has been used as a reliable electronic parameter to assess their σ-donating power. Furthermore, MESP topology analysis can be used to forecast the structure and energetics of lone pair π-complexes. The MESP approach to rationalize lone pair interactions in molecular systems has led to the design of cyclic imines for CO2 capture. The MESP topology analysis of intermolecular complexes revealed a hitherto unknown phenomenon in chemical bonding theory─formation of a covalent bond due to the influence of a noncovalent bond. The MESP-guided approach to intermolecular interactions provided a successful design strategy for the development of CO2 capture systems. The MESP parameters Vmin and MESP at the nucleus, Vn, derived for the molecular systems have been used as powerful measures for the extent of electron donor-acceptor (eDA) interactions in noncovalent complexes. Noncovalent bond formation leads to more negative MESP at the acceptor nucleus (VnA) and less negative MESP at the donor nucleus (VnD). The strong linear relationship observed between ΔΔVn = ΔVnD - ΔVnA and bond energy suggested that MESP data provide a clear evidence of bond formation. Furthermore, MESP topology studies established a cooperativity rule for understanding the donor-acceptor interactive behavior of a dimer D...A with a third molecule. According to this, the electron reorganization in the dimer due to the eDA interaction enhances electron richness at "A", the acceptor, and enhances electron deficiency at "D", the donor. Resultantly, D in D...A is more accepting toward trimer formation, while A in D...A is more donating. MESP topology offers promising design strategies to tune the electron-donating strength in various noncovalent interactions in hydrogen-, dihydrogen-, halogen-, tetrel-, pnicogen-, chalcogen-, and aerogen-bonded complexes and thereby to predict the interactive behavior of molecules. To sum up, MESP topology analysis has become one of the most effective modern techniques for understanding, interpreting, and predicting the intermolecular interactive behavior of molecules.

Accurate global machine learning force fields for molecules with hundreds of atoms.

Global machine learning force fields, with the capacity to capture collective interactions in molecular systems, now scale up to a few dozen atoms due to considerable growth of model complexity with system size. For larger molecules, locality assumptions are introduced, with the consequence that nonlocal interactions are not described. Here, we develop an exact iterative approach to train global symmetric gradient domain machine learning (sGDML) force fields (FFs) for several hundred atoms, without resorting to any potentially uncontrolled approximations. All atomic degrees of freedom remain correlated in the global sGDML FF, allowing the accurate description of complex molecules and materials that present phenomena with far-reaching characteristic correlation lengths. We assess the accuracy and efficiency of sGDML on a newly developed MD22 benchmark dataset containing molecules from 42 to 370 atoms. The robustness of our approach is demonstrated in nanosecond path-integral molecular dynamics simulations for supramolecular complexes in the MD22 dataset.

Thermophysical properties of 1-butyl-3-methylimidazolium octyl sulfate ionic liquid in aqueous and aqueous electrolyte solutions at different temperatures

Understanding the molecular interaction of 1-butyl-3-methylimidazolium octyl sulfate i.e., [Bmim][OcOSO3] in water and in aqueous NaCl solution is important for fabricating the new process. As it is already known that ionic liquids along with inorganic salt NaCl have significant potential in the tribology of lubricants and salting-out media for the separation of nicotine. It is known that ionic liquids exhibit characteristic behavior at solid−liquid interfaces. Although it is believed that the structure of ionic liquids at the interface contributes to the tribological properties in the region of boundary-mixed lubrication, this contribution has not been clarified yet. Thus, we study the molecular interaction of the ionic liquid in aqueous and ionic liquid in aqueous NaCl solutions through the thermodynamic approach. We have measured density as an important parameter for 1-butyl-3-methylimidazolium octyl sulfate i.e., [Bmim][OcOSO3] in water and in aqueous NaCl solution within the concentration range of 0.04-0.12 mol/kg at different temperatures i.e. 293.15, 298.15, 303.15, 308.15, and 313.15 K and atmospheric pressure by using a densitometer (DSA5000M Anton Paar). The density (ρ) data were employed to measure some derived parameters such as apparent molar volume of solute (Vϕ), limiting apparent molar volume of solute (Vϕ0), thermal expansion coefficient (α), apparent molar expansivity of solute at finite concentration (Eϕ) and at infinite concentration (Eϕ0) and transfer volume (ΔtrVϕ0). Results have been discussed in terms of all the possible molecular interactions in systems.

Synthesis, X-ray structure, antimicrobial activity, DFT and molecular docking studies of N-(thiophen-2-ylmethyl)thiophene-2-carboxamide.

In the present study, N-(thiophen-2-ylmethyl)thiophene-2-carboxamide, C10H9NOS2, (I), was obtained by the reaction of thiophene-2-carbonyl chloride and thiophen-2-ylmethanamine. Characterization of (I) was carried out using X-ray diffraction, spectroscopic techniques and elemental analyses. The DFT/B3LYP/6-311++G(d,p) theoretical level was successfully applied to calculate the optimized geometry and the local and global chemical activity parameters. The results obtained show good agreement between the experimental and theoretical geometrical parameters. The local and global chemical activity parameters were examined to determine the electrophilic and nucleophilic sites in (I). The natural bond orbital (NBO) analysis of (I) gives an efficient methodology for investigating the inter- and intramolecular bonding, as well as giving a convenient basis for investigating charge transfer or conjugative interactions in molecular systems. Also, the antimicrobial activity of (I) was investigated against eight microorganisms using the microdilution method and it is found to have an effective antibacterial activity. In addition, molecular docking studies were calculated in order to understand the nature of the binding of (I) with a lung cancer protein (PDB entry 1x2j).

Non-Covalent Interactions in Molecular Systems: Thermodynamic Evaluation of the Hydrogen-Bond Strength in Amino-Ethers and Amino-Alcohols.

The intramolecular hydrogen bond (intra‐HB) is one of the best‐known examples of non‐covalent interactions in molecules. Among the different types of intramolecular hydrogen bonding, the NH⋅⋅⋅O hydrogen bond in amino‐alcohols and amino‐ethers is one of the weakest. In contrast to the strong OH⋅⋅⋅N intramolecular hydrogen bond, the strength of the NH⋅⋅⋅O bond can hardly be measured with conventional spectroscopic methods, even for simple amino‐alcohols, since the band belonging to the NH⋅⋅⋅O conformer merges with the free OH band. In this work, we developed a combination of G4 calculations, and a method based on experimental vaporization enthalpies to determine the NH⋅⋅⋅O hydrogen bonding strength. The archetypal compounds for this study are 2‐amino‐1‐ethanol and 3‐amino‐1‐propanol as well as their respective methoxy analogs. Based on these molecules, different series were studied to investigate various factors influencing NH⋅⋅⋅O intra‐HB strength. In the first series, the influence of alkylation near the hydroxy or methoxy group and the amino group in sterically hindered aminoalcohols was examined. In the second series, the influence of alkylation of the amino‐group was investigated. In the third series, the effect of extending the alkyl chain between functional groups was studied.

Diagrammatics of tunable interactions in anisotropic colloids in rotating electric or magnetic fields: New kind of dipole-like interactions.

Anisotropic particles are widely presented in nature, from colloidal to bacterial systems, and control over their interactions is of crucial importance for many applications, from self-assembly of novel materials to microfluidics. Placed in rapidly rotating external electric fields, colloidal particles attain a tunable long-range and many-body part in their interactions. For spherical colloids, this approach has been shown to offer rich capabilities to construct the tunable interactions via designing the internal structure of particles and spatial hodographs of external rotating fields, but in the case of anisotropic particles, the interactions remain poorly understood. Here, we show that tunable interactions between anisotropic rod-like and spheroidal colloidal particles in rotating electric or magnetic fields can be calculated and analyzed with the diagrammatic technique we developed in the present work. With this technique, we considered an in-plane rotating electric field, obtained the long-range asymptotics of the anisotropic interactions, calculated the tunable interactions between particles rotating synchronously, and found conditions for rotator repulsion. We compared the mechanisms providing tunable interactions to those for orientational (Keesom), induction (Debye), and dispersion (London) interactions in molecular systems and found that the tunable interactions between anisotropic particles represent a novel kind of dipole-like interaction. The method can be directly generalized for magnetically induced interactions, 3D systems, and fields with spatial hodographs. The results provide significant advance in theoretical methods for tunable interactions in colloids and, therefore, are of broad interest in condensed matter, chemical physics, physical chemistry, materials science, and soft matter.

Non-covalent interactions in molecular systems: thermodynamic evaluation of the hydrogen bond strength in aminoalcohols.

In molecules with two functional groups that form hydrogen bonds, the structure-property relationship can depend significantly on the strength of intra-molecular hydrogen bonding. This bonding can cause a substantial conformational change that is accompanied by a frequency shift in the infrared spectrum, which provides the basis for experimental studies. Despite its great importance in biological systems, the available literature data for the strength of this bonding are scarce and not in agreement. In this work, we present the results of four thermodynamic methods for the determination of the strength of intramolecular hydrogen bonds. Comprehensive thermochemical analysis of 1-amino-2-alcohols and 2-amino-1-alcohols was performed with Fourier-transform infrared spectroscopy, high-level G4 quantum-chemical calculations, the homomorph scheme with enthalpies of vaporization and a group contribution method. With the combination of these four thermodynamic methods, the strength of intramolecular hydrogen bonding in 1,2-aminoalcohols and 2,1-aminoalcohols was evaluated quantitatively. The results were correlated with NBO parameters to find an explanation for the different strengths of intramolecular hydrogen bonds in total charge transfer and second order stabilization energies.

Volumetric and viscometric studies of molecular interactions in systems containing tartaric acid in water/aqueous-L-arginine solutions at 303.15 K

The densities and viscosities of aqueous solutions containing tartaric acid and L-Arginine were measured at 303.15 K. The densities were used to calculate the apparent molar volume of tartaric acid in water and aqueous-L-Arginine solutions. The apparent molar volumes were fitted to the linear fit Masson relation and relative viscosities were fitted to the Jones-Dole equation. From Masson relation, the partial molar volumes were determined and from Jones-Dole equation, the viscosity B-coefficients were determined. Strong solute-solvent interactions in aqueous solutions of tartaric acid solutions were observed from the transfer volumes and viscosity B-coefficient. The pH of these systems was also measured to understand the transfer of a proton from solute to cosolute. A weakening of solute-solvent interactions and loosening of the hydration sphere of tartaric acid on the addition of cosolute has been observed.

Hyperfine structure in the HD molecule

We investigate interactions between the proton spin, the deuteron spin, and the orbital angular momentum in the electronic ground state of the HD molecule. These interactions lead to hyperfine splittings of molecular energy levels. Our numerical results for the first rotational level agree well with the currently most accurate measurement performed by Ramsey {\em et al.} in the 1950s. Knowledge of the hyperfine structure of other levels is necessary for the accurate determination of rovibrational transition energies in spectroscopic measurements. We present theoretical predictions and share the numerical code used to perform numerical calculations. This work sets the ground for high precision spectroscopic tests of hyperfine interactions in molecular systems. In particular we determine the value of the deuteron quadrupole moment $Q = 0.2856(2)$ fm$^2$ and give outlook for improving its accuracy by three orders of magnitude.

Organic solar cells and physics education

This paper explains the operational principles of a home-made organic solar cell with the representation of an electron-cycle on an energy-level diagram. We present test data for a home-made organic solar cell which operates as a galvanic cell and current source in an electrical circuit. To determine the maximum power of the cell, the optimal current was estimated with a linear approximation. Using different light sources and dyes, the electrical properties of organic solar cells were compared. The solar cells were studied by looking at spectrophotometric data from different sensitizer dyes, generated by a do-it-yourself diffraction grating spectroscope. The sensitizer dyes of solar cells were tested by the diffraction grating spectroscope. The data were analysed on a light-intensity−wavelength diagram to discover which photons were absorbed and to understand the colours of the fruits containing these dyes. In terms of theoretical applications, the paper underlines the analogous nature of organic solar cells, a conventional single p−n junction solar cell and the light-dependent reactions of photosynthesis, using energy-level diagrams of electron-cycles. To conclude, a classification of photon−electron interactions in molecular systems and crystal lattices is offered, to show the importance of organic solar cells.

(13)C or Not (13)C: Selective Synthesis of Asymmetric Carbon-13-Labeled Platinum(II) cis-Acetylides.

Asymmetric isotopic labeling of parallel and identical electron- or energy-transfer pathways in symmetrical molecular assemblies is an extremely challenging task owing to the inherent lack of isotopic selectivity in conventional synthetic methods. Yet, it would be a highly valuable tool in the study and control of complex light-matter interactions in molecular systems by exclusively and nonintrusively labeling one of otherwise identical reaction pathways, potentially directing charge and energy transport along a chosen path. Here we describe the first selective synthetic route to asymmetrically labeled organometallic compounds, on the example of charge-transfer platinum(II) cis-acetylide complexes. We demonstrate the selective (13)C labeling of one of two acetylide groups. We further show that such isotopic labeling successfully decouples the two ν(C≡C) in the mid-IR region, permitting independent spectroscopic monitoring of two otherwise identical electron-transfer pathways, along the (12)C≡(12)C and (13)C≡(13)C coordinates. Quantum-mechanical mixing leads to intriguing complex features in the vibrational spectra of such species, which we successfully model by full-dimensional anharmonically corrected DFT calculations, despite the large size of these systems. The synthetic route developed and demonstrated herein should lead to a great diversity of asymmetric organometallic complexes inaccessible otherwise, opening up a plethora of opportunities to advance the fundamental understanding and control of light-matter interactions in molecular systems.

Functionalized fullerenes in water: a closer look.

The excellent photophysical properties of C60 fullerenes have spurred much research on their application to aqueous systems for biological and environmental applications. Spontaneous aggregation of C60 in water and the consequent diminution of photoactivity present a significant challenge to aqueous applications. The mechanisms driving the reduction of photoactivity in fullerene aggregates and the effects of functionalization on these processes, however, are not well understood. Here, we take a closer look at the molecular phenomena of functionalized fullerene interactions in water utilizing simulation and experimental tools. Molecular dynamic simulations were performed to investigate time-evolved molecular interactions in systems containing fullerenes with water, oxygen, and/or neighboring fullerene molecules, complimented by physical and chemical characterizations of the fullerenes pre- and postaggregation. Aggregates with widely different photoactivities exhibit similar fullerene-water interactions as well as surface and aggregation characteristics. Photoactive fullerene aggregates had weaker fullerene-fullerene and fullerene-O2 interactions, suggesting the importance of molecular interactions in the sensitization route.

Characterizing Molecular Interactions in Chemical Systems.

Interactions between atoms have a major influence on the chemical properties of molecular systems. While covalent interactions impose the structural integrity of molecules, noncovalent interactions govern more subtle phenomena such as protein folding, bonding or self assembly. The understanding of these types of interactions is necessary for the interpretation of many biological processes and chemical design tasks. While traditionally the electron density is analyzed to interpret the quantum chemistry of a molecular system, noncovalent interactions are characterized by low electron densities and only slight variations of them--challenging their extraction and characterization. Recently, the signed electron density and the reduced gradient, two scalar fields derived from the electron density, have drawn much attention in quantum chemistry since they enable a qualitative visualization of these interactions even in complex molecular systems and experimental measurements. In this work, we present the first combinatorial algorithm for the automated extraction and characterization of covalent and noncovalent interactions in molecular systems. The proposed algorithm is based on a joint topological analysis of the signed electron density and the reduced gradient. Combining the connectivity information of the critical points of these two scalar fields enables to visualize, enumerate, classify and investigate molecular interactions in a robust manner. Experiments on a variety of molecular systems, from simple dimers to proteins or DNA, demonstrate the ability of our technique to robustly extract these interactions and to reveal their structural relations to the atoms and bonds forming the molecules. For simple systems, our analysis corroborates the observations made by the chemists while it provides new visual and quantitative insights on chemical interactions for larger molecular systems.

A Comparative Study of Transferable Aspherical Pseudoatom Databank and Classical Force Fields for Predicting Electrostatic Interactions in Molecular Dimers.

Accurate and fast evaluation of electrostatic interactions in molecular systems is one of the most challenging tasks in the rapidly advancing field of macromolecular chemistry and drug design. Electrostatic interactions are of crucial importance in biological systems. They are well represented by quantum mechanical methods; however, such calculations are computationally expensive. In this study, we have evaluated the University of Buffalo Pseudoatom Databank (UBDB)1,2 approach for approximation of electrostatic properties of macromolecules and their complexes. We selected the S663 and JSCH-20054 data sets (208 molecular complexes in total) for this study. These complexes represent a wide range of chemical and biological systems for which hydrogen bonding, electrostatic, and van der Waals interactions play important roles. Reference electrostatic energies were obtained directly from wave functions at the B3LYP/aug-cc-pVTZ level of theory using the SAPT (Symmetry-Adapted Perturbation Theory) scheme for calculation of electrostatic contributions to total intermolecular interaction energies. Electrostatic energies calculated on the basis of the UBDB were compared with corresponding reference results. Results were also compared with energies computed using a point charge model from popular force fields (AM1-BCC and RESP used in AMBER and CGenFF from CHARMM family). The energy trends are quite consistent (R2 ≈ 0.98) for the UBDB method as compared to the AMBER5 and CHARMM force field methods6(R2 ≈ 0.93 on average). The RSMEs do not exceed 3.2 kcal mol–1 for the UBDB and are in the range of 3.7–7.6 kcal mol–1 for the point charge models. We also investigated the discrepancies in electrostatic potentials and magnitudes of dipole moments among the tested methods. This study shows that estimation of electrostatic interaction energies using the UBDB databank is accurate and reasonably fast when compared to other known methods, which opens potential new applications to macromolecules.

Zero-multipole summation method for efficiently estimating electrostatic interactions in molecular system

The zero-multipole summation method has been developed to efficiently evaluate the electrostatic Coulombic interactions of a point charge system. This summation prevents the electrically non-neutral multipole states that may artificially be generated by a simple cutoff truncation, which often causes large amounts of energetic noise and significant artifacts. The resulting energy function is represented by a constant term plus a simple pairwise summation, using a damped or undamped Coulombic pair potential function along with a polynomial of the distance between each particle pair. Thus, the implementation is straightforward and enables facile applications to high-performance computations. Any higher-order multipole moment can be taken into account in the neutrality principle, and it only affects the degree and coefficients of the polynomial and the constant term. The lowest and second moments correspond respectively to the Wolf zero-charge scheme and the zero-dipole summation scheme, which was previously proposed. Relationships with other non-Ewald methods are discussed, to validate the current method in their contexts. Good numerical efficiencies were easily obtained in the evaluation of Madelung constants of sodium chloride and cesium chloride crystals.

Ultrafast Charge Transfer through Noncovalent Au–N Interactions in Molecular Systems

Charge transfer through noncovalent interactions is crucial to a variety of chemical phenomena. These interactions are often weak and nonspecific and can coexist, making it difficult to isolate the transfer efficiency of one type of bond versus another. Here, we show how core-hole clock spectroscopy can be used to measure charge transfer through noncovalent interactions. We study the model system 1,4-benzenediamine molecules bound on an Au surface through an Au–N donor–acceptor bond as these are known to provide a pathway for electronic conduction in molecular devices. We study different phases of the molecule/Au system and map charge delocalization times from carbon and nitrogen sites on the molecule. We show that charge delocalization across Au–N donor–acceptor bond occurs in less than 500 as. Furthermore, the Au–N bond also enhances delocalization times from neighboring carbon sites, demonstrating that fast charge transfer across a metal–organic interface does not require a covalently bonded system.