Charge Distribution In Molecules Research Articles

Unveiling field-coupled nanocomputing: Leaning molecules to shape readable bits

Molecular field-coupled nanocomputing (molFCN) encodes information in the molecule charge distribution and elaborates it through electrostatic coupling. Despite the advantageous sub-nanometric size and low-power dissipation, only a few attempts have been made to validate the technology experimentally. One of the obstacles is the difficulty in measuring molecule charges to validate information encoding or integrate molFCN with complementary-metal-oxide-semiconductor (CMOS). In this work, we propose a paradigm preserving the advantages of molFCN, which exploits the position of waiving molecules to augment the information encoding. We validate the paradigm, named bend-boosted molFCN, with density functional theory using 6-(ferrocenyl)hexanethiol cations. We demonstrate that the encoded information can be electrically read by constituting a molecular junction. The paradigm is compatible with the charge-based molFCN, thus acting as a readout system. The obtained results favor the experimental assessment of the molFCN principle through scanning probe microscopy techniques and the design of molFCN-CMOS heterogeneous circuits.

Bistriazolotriazole-tetramine: commendable energetic moiety and cation.

Various 7H,7'H-[6,6'-bi[1,2,4]triazolo[4,3-b][1,2,4]triazole]-3,3',7,7'-tetramine (A) based nitrogen-rich energetic salts were designed and their properties explored. All energetic salts possess relatively high nitrogen content (> 48%), positive heats of formation (> 429kJ/mol) and stability owing to a significant contribution from fused backbone. The cationic component shows a very high heat of formation (2516kJ/mol); therefore, it is highly suitable for enthalpy enhancement in new energetic salts. The cation was paired with the energetic anions nitrate (NO3-), perchlorate (ClO4-), dinitromethanide (CH(NO2)2-), trinitromethanide (C(NO2)3-), nitroamide (NHNO2-), and dinitroamide (N(NO2)2-) to improve oxygen balance and detonation performance. Designed salts show moderate detonation velocities (7.9-8.7 km/s) and pressures (23.8 - 33.1 GPa). The distribution of frontier molecular orbitals, molecular electrostatic surface potentials, QTAIM topological properties, and noncovalent interactions of designed salts were simulated to understand the electronic structures, charge distribution in molecules, hydrogen bonding, and other nonbond interactions. The predicted safety factor (SF) and impact sensitivity (H50) of designed salts suggest their insensitivity to mechanical stimuli. This work explored the 7H,7'H-[6,6'-bi[1,2,4]triazolo[4,3-b][1,2,4]triazole]-3,3',7,7'-tetramine as a suitable cationic component which could be promising and serve exemplarily in energetic materials. The optimization and energy calculations of all the designed compounds were carried out at the B3LYP/6-311 + + G(d,p) and M06-2X/def2-TZVPP levels, utilizing the Gaussian software package. The molecular surface electrostatic potential, quantum theory of atoms in molecules (QTAIM), reduced density gradient (RDG), and noncovalent interaction (NCI) analysis were performed by employing Multiwfn software. The EXPLO5 (v 7.01) thermochemical code and PILEM web application were used to predict the detonation properties.

Quantum computations of non-steroidal anti-inflammatory drug molecules using Density Functional Theory

This paper addresses the electronic states and physicochemical properties of non-steroidal anti-inflammatory drug (NSAID) namely: Ibuprofen, Ketoprofen and Flufenamic acid. The molecular structures are quantum chemically treated and geometrically optimised using density functional theory (DFT). The computed geometrical parameters are compared with the experimental data. The Mulliken charge analysis is accomplished to understand the partial charge distribution in molecules. The molecular electrostatic potential analysis has been used to identify the appropriate location for an electrophilic and nucleophilic attacking site. Frontier molecular orbitals of the molecules are estimated and analysed. The HOMO-LUMO energy gaps have been used to estimate the different global reactivity descriptors of the selected molecules under investigation. The FT-IR spectra of molecules are recorded experimentally and are computed using DFT. The potential energy distribution (PED) assignment for the computed vibrations is carried out. The NBO analysis has been used to find the most intensive interaction in molecules based on the Fock-matrix sta3bilization energy. The NLO parameters have been computed for molecules to check their suitability towards NLO based applications. The UV-absorption spectra and ADME parameters for titled molecules are also simulated.

Quantum Computational, Spectroscopic (FT-IR, FT-Raman, NMR, and UV-Vis) Hirshfeld Surface and Molecular Docking-Dynamics Studies on 5-Hydroxymethyluracil (Monomer and Trimer).

For many decades, uracil has been an antineoplastic agent used in combination with tegafur to treat various human cancers, including breast, prostate, and liver cancer. Therefore, it is necessary to explore the molecular features of uracil and its derivatives. Herein, the molecule's 5-hydroxymethyluracil has been thoroughly characterized by NMR, UV-Vis, and FT-IR spectroscopy by means of experimental and theoretical analysis. Density functional theory (DFT) using the B3LYP method at 6-311++G(d,p) was computed to achieve the optimized geometric parameters of the molecule in the ground state. For further investigation and computation of the NLO, NBO, NHO analysis, and FMO, the improved geometrical parameters were utilized. The potential energy distribution was used to allocate the vibrational frequencies using the VEDA 4 program. The NBO study determined the relationship between the donor and acceptor. The molecule's charge distribution and reactive regions were highlighted using the MEP and Fukui functions. Maps of the hole and electron density distribution in the excited state were generated using the TD-DFT method and PCM solvent model in order to reveal electronic characteristics. The energies and diagrams for the lowest unoccupied molecular orbital (LUMO) and the highest occupied molecular orbital (HOMO) were also provided. The HOMO-LUMO band gap estimated the charge transport within the molecule. When examining the intermolecular interactions in 5-HMU, Hirshfeld surface analysis was used, and fingerprint plots were also produced. The molecular docking investigation involved docking 5-HMU with six different protein receptors. Molecular dynamic simulation has given a better idea of the binding of the ligand with protein.

Investigation of solid–liquid equilibrium and thermodynamic models of D-Tagatose in mono-solvents and binary solvents

As a rare sugar, D-Tagatose is regarded as an excellent low-energy food sweetener. It is especially beneficial for physical health, such as inhibiting hyperglycemia, improving intestinal flora, and avoiding caries. It is broadly employed in food, medicine, cosmetics, and other fields. Acquiring D-Tagatose solubility is vital to develop D-Tagatose crystallization process to obtain high-quality D-Tagatose production. In this study, the solubility of D-Tagatose in seven pure solvents (methanol, ethanol, n-propanol, water, N, N-dimethylformamide, dimethyl sulfoxide, N-methylpyrrolidone), three binary solvents (ethanol-water mixtures, ethanol-methanol mixtures, and n-propanol-water mixtures) was determined by HPLC method at temperatures from 293.15 K to 323.15 K. Then, the Van't Hoff equation, Apelblat equation, λh equation, NRTL equation, CNIBS/Redlich-Kister model and modified Jouyban-Acree-van't Hoff model were used to correlate the solubility. The correlated solubility accounted for suitable compatibility with the experimental results (ARD <10%). Furthermore, we investigated the intermolecular interactions in the crystal structure through Hirshfeld surface analysis and estimated the overall charge distribution of molecules by molecular electrostatic potential surface (MEPs). Then, we analyzed the solvent effects and solvation free energy to explain the solubility behaviors. The results indicated that hydrogen bonds play a decisive role in determining the solubility of D-Tagatose.

Investigations on experimental, theoretical spectroscopic, electronic excitations, molecular docking of Sulfaguanidine (SG): An antibiotic drug

Sulfaguanidine is an antibiotic drug. The FT-IR, UV–Vis, 1H NMR, 13C NMR spectra were recorded and analyzed. Optimized geometry and vibrational modes were theoretically calculated by the DFT approach. Detailed analysis on fundamental modes and vibrational frequencies was carried out. Electron excitation analysis via Hole and Electron density distribution mapping in 3 different excited states was carried out. NBO has been carried out to elucidate the hybrid structure. MEP analysis was carried out to demonstrate charge distribution in molecules. The bioactivity of the molecule is calculated theoretically with the help of the electrophilicity index. Molecular docking of SG was carried out with six different protein receptors.

Computational Quantum Chemical Study, Insilco ADMET, and Molecular Docking Study of 2-Mercapto Benzimidazole

The title compound 2-mercapto benzimidazole (MBI) was deliberated optimal structure, data were calculated using the density functional theory (DFT) B3LYP method on 6-311++G (d, p) basis set. The structural parameters were derived from geometry optimization and compared with experimental parameters. The HOMO and LUMO energies are calculated for the title molecule. NBO analysis was carried out to identify the internal molecular electronic interactions and their stabilizing energies. The DFT has been used to deduce the properties like polarizability (α), dipole moment (μ), and first hyperpolarizability (β). Electrostatic potential plotting with iso-surface plot (MESP) and the mappings of electron density with molecular electrostatic potential has been constructing for the concept of charge distribution in molecules as the sites of nucleophilic reactions and electrophilic effect. Header compound has greater drug-likeness and ADMET proficiency. Molecular docking simulations have been analyzed to identify the binding affinity of the title compound with Covid-19 protein (5R7Y).

Ab initio Molecular Dynamics Simulations of Field-Coupled Nanocomputing Molecules

Molecular Field-Coupled Nanocomputing (FCN) represents one of the most promising solutions to overcome the issues introduced by CMOS scaling. It encodes the information in the molecule charge distribution and propagates it through electrostatic intermolecular interaction. The need for charge transport is overcome, hugely reducing power dissipation.At the current state-of-the-art, the analysis of molecular FCN is mostly based on quantum mechanics techniques, or ab initio evaluated transcharacteristics. In all the cases, studies mainly consider the position of charges/atoms to be fixed. In a realistic situation, the position of atoms, thus the geometry, is subjected to molecular vibrations. In this work, we analyse the impact of molecular vibrations on the charge distribution of the 1,4-diallyl butane. We employ Ab Initio Molecular Dynamics to provide qualitative and quantitative results which describe the effects of temperature and electric fields on molecule charge distribution, taking into account the effects of molecular vibrations. The molecules are studied at near-absolute zero, cryogenic and ambient temperature conditions, showing promising results which proceed towards the assessment of the molecular FCN technology as a possible candidate for future low-power digital electronics. From a modelling perspective, the diallyl butane demonstrates good robustness against molecular vibrations, further confirming the possibility to use static transcharacteristics to analyse molecular circuits.

Quantitative explanation of the Schottky barrier height

Eight decades ago, Schottky proposed that the energy barrier at the metal-semiconductor interface, which now bears his name, should be compared with the difference of two surface quantities, the work function (WF) of the metal and the ionization potential of the semiconductor. This tradition of plotting and modeling the Schottky barrier height (SBH) against the metal WF has been followed ever since. However, success in general quantitative understanding of the SBH from physical principles has been limited, and empirical models are still relied upon. Here, we show that the stumbling block that has prevented a broadly applicable physical explanation of the SBH is the presence of surface dipole terms, inherently included in the traditional, Schottky-Mott styled analyses. By removing these surface contributions with the help of the recently developed neutral polyhedra theory, we show that the SBHs calculated for a very large number of epitaxial interfaces between metals and zinc-blende semiconductors are quantitatively explained from general chemical principles. Amazingly, SBHs calculated for 17 different semiconductors fit onto the same universal plot. Previously, SBHs needed to be grouped according to the semiconductor before analyses could be conducted separately for, and with empirical parameters specific to, each semiconductor. This work shows that the mechanism for SBH formation at metal-semiconductor interface is none other than the same chemistry responsible for charge distribution in molecules. There is no need for empirical modeling once the traditional beginning-point of SBH analysis is abandoned and the proposed new one is used.

IR and Raman spectra with Gaussian-09 molecular analysis of some other parameters and vibrational spectra of 5-fluoro-uracil

Recorded IR and Raman spectra of 5-fluoro-uracil have been analyzed with the carried out theoretical computation by Gaussian-09 [DFT/B3LYP/6-311 ++G**] and GAR2PED software. In the assignment of fundamental modes, the GAR2PED software has been used to calculate the PEDs. HOMO–LUMO energy gap study supports the possibility of charge transfer in biomolecule. Electrostatic potential plotting with iso-surface plot and the mappings of electron density with molecular electrostatic potential have been made for the concept of charge distribution in molecules as the sites of nucleophilic reactions and electrophilic effect. The DFT calculations have been employed to yield the atomic polarizability tensor charges, Mulliken atomic charges, molecular structure and thermodynamic functional properties of the biomolecule. The assignment has been made in the two species for the normal mode of the fluoro group substituent on pyrimidine ring.

Intermolecular interactions play a role in the distribution and transport of charged contrast agents in a cartilage model.

The transport and distribution of charged molecules in polyelectrolyte solutions are of both fundamental and practical importance. A practical example, which is the specific subject addressed in the present paper, is the transport and distribution of charged species into cartilage. The charged species could be a contrast agent or a drug molecule involved in diagnosis or treatment of the widespread degenerative disease osteoarthritis, which leads to degradation of articular cartilage. Associated scientific issues include the rate of transport and the equilibrium concentrations of the charged species in the cartilage and the synovial fluid. To address these questions, we present results from magnetic resonance micro-imaging experiments on a model system of articular cartilage. The experiments yield temporally and spatially resolved data on the transport of a negatively charged contrast agent (charge = -2), used in medical examinations of cartilage, into a polyelectrolyte solution, which is designed to capture the electrostatic interactions in cartilage. Also presented is a theoretical analysis of the transport where the relevant differential equations are solved using finite element techniques as well as treated with approximate analytical expressions. In the analysis, non-ideal effects are included in the treatment of the mobile species in the system. This is made possible by using results from previous Monte Carlo simulations. The results demonstrate the importance of taking non-idealities into account when data from measurements of transport of charged solutes in a system with fixed charges from biological polyelectrolytes are analyzed.

Deep core photoionization of iodine in CH3I and CF3I molecules: how deep down does the chemical shift reach?

Hard X-ray electron spectroscopic study of iodine 1s and 2s photoionization of iodomethane (CH3I) and trifluoroiodomethane (CF3I) molecules is presented. The experiment was carried out at the SPring-8 synchrotron radiation facility in Japan. The results are analyzed with the aid of relativistic molecular and atomic calculations. It is shown that charge redistribution within the molecule is experimentally observable even for very deep levels and is a function of the number of electron vacancies. We also show that the analysis of Auger spectra subsequent to hard X-ray photoionization can be used to provide insight into charge distribution in molecules and highlight the necessity of quantum electrodynamics corrections in the prediction of core shell binding energies in molecules that contain heavy atoms.

Excess Spectroscopy: Concept and Applications

Excess spectroscopy was proposed following the idea of excess thermodynamic functions. It is complementary to classical excess functions because it provides rich information on molecular interactions. In this review, we introduce in detail the concept of excess spectroscopy and the measurement of excess spectra for the case of infrared spectroscopy. We then describe the merits of using excess spectroscopy to enhance apparent spectral resolution, judge the non-ideality of mixtures, determine the selectivity of molecular interactions, identify distinct species or clusters in solutions, and provide information related to charge distributions in molecules. Following this, we review the progress in methodology where excess spectroscopy is extended to partial molar excess spectroscopy and Raman spectroscopy. The extension of binary mixtures to pseudo binary mixtures and/or liquid samples to solid samples is also described. Finally, we discuss several recent applications of excess spectroscopy in the study of hydrogen-bonding interactions in ionic liquidmolecular solvent systems, halogen-bonding interactions in benzene derivative-dimethylsulfoxide (DMSO) mixtures, and interactions between inorganic cations/anions and water molecules. Clearly, excess spectroscopy has opened a new window through which we can view rich information about molecular interactions. 物理化学学报(Wuli Huaxue Xuebao) January Acta Phys. -Chim. Sin. 2016, 32 (1), 239–248 239 [Review] doi: 10.3866/PKU.WHXB201511241 www.whxb.pku.edu.cn Received: October 19, 2015; Revised: November 23, 2015; Published on Web: November 24, 2015. *Corresponding author. Email: yuzhw@mail.tsinghua.edu.cn; Tel: +86-10-62792492. The project was supported by the National Natural Science Foundation of China (21133009, 21473099). 国家自然科学基金(21133009, 21473099)资助项目 ©Editorial office of Acta Physico-Chimica Sinica

The use of COSMO-SAC to predict relative adhesion between polymer matrices and silane-treated glass surfaces in filled particulate composites

Successful efforts have been made at predicting the adhesion between several polymer matrices and the surface of a glass filler, treated with various coupling agents using thermodynamic descriptors. A good thermodynamic criterion has been shown to be the (negative) Gibbs free energy of mixing (−ΔGmix)0.5, for a solution containing molecules representative of the repeat units of the polymer and the exposed functional groups of the silane coupling agents. Group contribution methods, such as UNIFAC allow for straightforward calculations of (−ΔGmix)0.5; however, the UNIFAC database remains incomplete, and furthermore requires a subscription to access the most current database. Recently, new predictive models based on the surface charge distribution of molecules and statistical thermodynamics have been developed to predict properties of solutions. In this work, one such method, COSMO-SAC, is used to calculate (−ΔGmix)0.5 and compare the results to a previously determined database of relative practical adhesion strengths between various polymer matrices and the organo-functional groups of silane coupling agents. The results obtained from COSMO-SAC show good agreement with the experimental database, except for the cases of significant steric effects and systems containing amines. Overall, the adhesion predictions obtained from COSMO-SAC calculations are comparable to the UNIFAC predictions, although UNIFAC was more successful in predicting adhesion for the amine containing compounds.

Introducing Charge Hydration Asymmetry in the Realm of Continuum Solvation

Charge hydration asymmetry (CHA) manifests itself in the experimentally observed strong dependence of free energy of ion hydration on the sign of the ion charge. This asymmetry is not consistently accounted for by popular models of solvation; its magnitude varies greatly between the models. While it is clear that CHA is somehow related to charge distribution within a water molecule, the exact nature of this relationship is unknown. We propose a simple, yet general and rigorous criterion that relates rotational and charge inversion properties of a water molecule's charge distribution with its ability to cause CHA. We show which electric multipole components of a water molecule are key to explain its ability for asymmetric charge hydration. We then test several popular water models and explain why specific models show none, little, or strong CHA in simulations. We use the gained insight to derive an analogue of the Born equation that includes the missing physics necessary to account for CHA and does not rely on redefining the continuum dielectric boundary. The proposed formula is as simple as the original, does not contain any fitting parameters, and predicts hydration free energies and entropies of spherical cations and anions within experimental uncertainty. We further incorporate CHA into the framework of Generalized Born continuum solvation model; our findings suggest that the gap between the practical continuum electrostatics framework and the more fundamental explicit solvent treatment can be reduced considerably by explicitly introducing CHA into the existing framework.

Multiple drugs and multiple targets: An analysis of the electrostatic determinants of binding between non‐nucleoside HIV‐1 reverse transcriptase inhibitors and variants of HIV‐1 RT

We present a systematic, computational analysis of the electrostatic component of binding of three HIV-1 RT inhibitors-nevirapine (NVP), efavirenz (EFV), and the recently approved rilpivirine (RPV)-to wild-type (WT) and mutant variants of RT. Electrostatic charge optimization was applied to determine how suited each molecule's charge distribution is for binding WT and individual mutants of HIV-1 RT. Although the charge distributions of NVP and EFV are rather far from being optimal for tight binding, RPVs charge distribution is close to the theoretical, optimal charge distribution for binding WT HIV-1 RT, although slight changes in charge can dramatically impact binding energetics. Moreover, toward the L100I/K103N double mutant, RPVs charge distribution is quite far from optimal. We also determine the contributions of chemical moieties on each molecule toward the electrostatic component of binding and show that different regions of a drug molecule may be used for recognition by different RT variants. The electrostatic contributions of certain RT residues toward drug binding are also computed to highlight critical residues for each interaction. Finally, the charge distribution of RPV is optimized to promiscuously bind to three RT variants rather than to each one in turn, with the resulting charge distribution being a compromise between the optimal charge distributions to each individual variant. Taken together, this work demonstrates that even in a binding site considered quite hydrophobic, electrostatics play a subtle yet varying role that must be considered in designing next-generation molecules that recognize rapidly mutating targets.

First-principles study of strong rectification and negative differential resistance induced by charge distribution in single molecule

For molecule-scale transport systems, a mechanism that the charge distribution of molecule under the various bias voltages can induce strong effect of rectification and negative differential resistance is proposed. Based on nonequilibrium Green's function combined with density functional theory, the proposal is testified by performing the first-principles calculations of transport characteristics of 2-(4(')-thiolate-butyl)-6-thiol-anthrecene molecule sandwiched in two gold electrodes. The strong effect of rectification and negative differential resistance is obtained. The rectification effect is as large as 16.

The QSAR Modeling of Cytotoxicity on Anthraquinones

AbstractA QSAR analysis was carried out on a dataset of 126 anthraquinone‐based cytotoxic compounds. A PCA of the molecular descriptors was used to cluster the dataset into smaller subsets according to their structural features and QSAR models were derived for the selected sets. During the modeling, protonated states of molecules and nonlinear transformations of the descriptors were considered. The developed models have been interpreted in the context of cytotoxicity and validated with leave‐one‐out, and leave‐many‐out cross‐validation. The descriptors in the resulting models describe the size and charge distribution of molecules although in different clusters their proportions vary.

In Silico Prediction of Medium Effects on Esterification Equilibrium Using the COSMO-RS Method

This paper presents a new approach for predicting solvent effects on esterification reactions of industrial importance in the field of biocatalysis. The COSMO-RS method has been used to calculate the activity coefficients of the chemical species involved in various reactions, carried out in different solvents. For comparison we also used the traditional UNIFAC method. Three lipase-catalyzed esterifications were considered: (1) 1-dodecanoic acid with menthol in n-hexane, n-heptane, cyclohexane, 2,2,4-trimethylpentane, toluene, acetonitrile, and 2-methyl-2-butanol; (2) 1-dodecanoic acid and 1-dodecanol in n-hexane, n-heptane, cyclohexane, 2,2,4-trimethylpentane, and toluene; and (3) glycerol and n-octanoic acid in acetonitrile, benzene, and toluene and in the neat reaction mixture (without any solvent). Predicted activities were used to calculate the thermodynamic equilibrium ratio. This should be independent of medium, and the variation in COSMO-RS values is at most 9-fold (corresponding to a DeltaG degrees of about 5.5 kJ/mol, which would still be a very useful prediction) and often only 2-fold (corresponding to less than 2 kJ/mol or 0.5 kcal/mol, therefore comparable with experimental error). UNIFAC is weaker, especially when important roles are played by conformational freedom, intramolecular interactions, strong polar effects, and charge distribution of molecules in the mixture. The relative percent deviations from the mean of equilibrium constants in different solvents range between 17 and 49 for COSMO-RS versus 32 to 65 for UNIFAC. The COSMO-RS method opens up new perspectives for the development of theoretical models for solvent selection with general applicability.

Atomic Charge Parameters for the Finite Difference Poisson-Boltzmann Method Using Electronegativity Neutralization.

An optimization of Rappe and Goddard's charge equilibration (QEq) method of assigning atomic partial charges is described. This optimization is designed for fast and accurate calculation of solvation free energies using the finite difference Poisson-Boltzmann (FDPB) method. The optimization is performed against experimental small molecule solvation free energies using the FDPB method and adjusting Rappe and Goddard's atomic electronegativity values. Using a test set of compounds for which experimental solvation energies are available and a rather small number of parameters, very good agreement was obtained with experiment, with a mean unsigned error of about 0.5 kcal/mol. The QEq atomic partial charge assignment method can reflect the effects of the conformational changes and solvent induction on charge distribution in molecules. In the second section of the paper we examined this feature with a study of the alanine dipeptide conformations in water solvent. The different contributions to the energy surface of the dipeptide were examined and compared with the results from fixed CHARMm charge potential, which is widely used for molecular dynamics studies.