Water Dimer Research Articles

Room for improvement in the initial martini 3 parameterization of peptide interactions

The Martini 3 coarse-grain force field has greatly improved upon its predecessor, having already been successfully employed in several applications. Here, we gauge the accuracy of Martini 2 and 3 protein interactions in two types of systems: coiled coil peptide dimers in water and transmembrane peptides. Coiled coil dimers form incorrectly under Martini 2 and not at all under Martini 3. With transmembrane peptides, Martini 3 represents better the membrane thickness–peptide tilt relationship, but shorter peptides do not remain transmembranar. We discuss related observations, and describe mitigation strategies involving either scaling interactions or restraining the system.

Solvent Induced Proton Polarization within the Nuclear−Electronic Orbital Framework

To explicitly account for nuclear quantum effects and solvent environments in simulations of chemical processes, the nuclear-electronic orbital approach is coupled with a polarizable continuum model (PCM). This NEO-PCM approach is used to explore the influence of solvation on nuclear polarization through applications to a water dimer and a set of protonated water tetramers. Nuclear polarization in these species is analyzed in terms of changes in proton density and oxygen-hydrogen bond length. Solvation is shown to enhance nuclear polarization with increasing dielectric constant. For the water dimer, the internal, hydrogen-bonded proton is shown to polarize more than the external, free proton. Moreover, proton quantization leads to greater solvent polarization through their mutual polarization. These calculations highlight the complex interplay among electronic, nuclear, and solvent polarization in chemical systems.

Energy natural orbital characterization of nonadiabatic electron wavepackets in the densely quasi-degenerate electronic state manifold.

Dynamics and energetic structure of largely fluctuating nonadiabatic electron wavepackets are studied in terms of Energy Natural Orbitals (ENOs) [K. Takatsuka and Y. Arasaki, J. Chem. Phys. 154, 094103 (2021)]. Such huge fluctuating states are sampled from the highly excited states of clusters of 12 boron atoms (B12), which have densely quasi-degenerate electronic excited-state manifold, each adiabatic state of which gets promptly mixed with other states through the frequent and enduring nonadiabatic interactions within the manifold. Yet, the wavepacket states are expected to be of very long lifetimes. This excited-state electronic wavepacket dynamics is extremely interesting but very hard to analyze since they are usually represented in large time-dependent configuration interaction wavefunctions and/or in some other complicated forms. We have found that ENO gives an invariant energy orbital picture to characterize not only the static highly correlated electronic wavefunctions but also those time-dependent electronic wavefunctions. Hence, we first demonstrate how the ENO representation works for some general cases, choosing proton transfer in water dimer and electron-deficient multicenter chemical bonding in diborane in the ground state. We then penetrate with ENO deep into the analysis of the essential nature of nonadiabatic electron wavepacket dynamics in the excited states and show the mechanism of the coexistence of huge electronic fluctuation and rather strong chemical bonds under very random electron flows within the molecule. To quantify the intra-molecular energy flow associated with the huge electronic-state fluctuation, we define and numerically demonstrate what we call the electronic energy flux.

H2O·HF@C70: Encapsulation Energetics and Thermodynamics

This report deals with the quantum-chemical evaluation of the energetics and thermodynamics of the simultaneous encapsulation of HF and H2O by the IPR (isolated pentagon rule) C70 fullerene cage, yielding H2O·HF@C70 species which were synthesized and characterized recently, thus further expanding the family of fullerene endohedrals with non-metallic encapsulates. The structures were optimized at the DFT (density functional theory) M06-2X/6-31++G** level. The encapsulation energetics were further refined by the advanced B2PLYPD/6-31++G** and B2PLYPD/6-311++G** methods. After enhancement of the B2PLYPD/6-311++G** encapsulation energy for the BSSE and steric corrections, the encapsulation energy gain was obtained, as 26 kcal/mol. The equilibrium encapsulation thermodynamics were described using the M06-2X/6-31++G** partition functions. The results correspond to our previous evaluations for the water dimer encapsulation by C84 cages.

Computing excited OH stretch states of water dimer in 12D using contracted intermolecular and intramolecular basis functions.

Due to the ubiquity and importance of water, water dimer has been intensively studied. Computing the (ro-)vibrational spectrum of water dimer is challenging. The potential has eight wells separated by low barriers, which makes harmonic approximations of limited utility. A variational approach is imperative, but difficult because there are 12 coupled vibrational coordinates. In this paper, we use a product contracted basis whose functions are products of intramolecular and intermolecular functions computed using an iterative eigensolver. An intermediate matrix F facilitates calculating matrix elements. Using F, it is possible to do calculations on a general potential without storing the potential on the full quadrature grid. We find that surprisingly many intermolecular functions are required. This is due to the importance of coupling between inter- and intra-molecular coordinates. The full G16 symmetry of water dimer is exploited. We calculate, for the first time, monomer excited stretch states and compare P(1) transition frequencies with their experimental counterparts. We also compare with experimental vibrational shifts and tunneling splittings. Surprisingly, we find that the largest tunneling splitting, which does not involve the interchange of the two monomers, is smaller in the asymmetric stretch excited state than in the ground state. Differences between levels we compute and those obtained with a [6+6]D adiabatic approximation [Leforestier et al. J. Chem. Phys. 137 014305 (2012)] are ∼0.6 cm-1 for states without monomer excitation, ∼4 cm-1 for monomer excited bend states, and as large as ∼10 cm-1 for monomer excited stretch states.

Estrogenic Effect Mechanism and Influencing Factors for Transformation Product Dimer Formed in Preservative Parabens Photolysis

The environmental transformation and health effects of endocrine disruptors (EDCs) need urgent attention, particularly the formation of transformation products with higher toxicity than parent EDCs. In this paper, an important transformation product dimer (short for ethyl 4-hydroxy-3-(2-((4-hydroxybenzoyl) oxy) ethyl) benzoate) with estrogenic activity was investigated and detected in the photolysis of preservative ethyl-paraben (EPB) dissolved in actual water. The environmental factors, such as the higher initial concentration of EPB, the stronger optical power and the lower pH could stimulate the formation of the dimer. Simultaneously, the interaction of multiple environmental factors was significant, especially the initial concentration and pH using the response surface methodology. Furthermore, the relationship between the environmental factors and the formation of the product dimer was further explained and the empirical model equation was built for predicting the amount of dimer in actual water. Quantum chemical and toxicological calculations showed the estrogenic effect mechanism of the product dimer and it was revealed further that the hydrogen bonds of the dimer and ERα proteins (ARG-394, Glu-353, His-524, GYY-521) were formed, with a lowest binding energy of -8.38 Kcal/mol during molecular docking. In addition, the health effect risk of the product dimer was higher than the parent compound in the blood, cardiovascular system, gastrointestinal system, kidney and liver. In short, the present study was of great significance for the transformation product in pollution control and health effects in the photolysis of EDCs.

Do-It-Yourself 5-Color 3D Printing of Molecular Orbitals and Electron Density Surfaces

This report outlines an approach for preparing 5-color 3D printed plastic models of molecular orbitals and electron density surfaces using a hobby-grade 3D printer. Instructions are provided for preparing 3D orbital and electron density surface (EDS) models using solid or mesh representations in ground state and transition state structures. We show that the information content of 3D orbital and surface models can be enhanced with text annotation, bisection, strut and dashed bond placement, and composite orbital-EDS model constructions. Example prints illustrate orbital concepts in organic and inorganic chemistry, such as the ethyl cation (σ–p hyperconjugation), methane (hybridization and C–H bonding), ethane (σ–σ* hyperconjugation in the staggered and eclipsed conformations), 2-hydroxytetrahydropyran (the anomeric effect/n−σ* hyperconjugation), the water dimer (hydrogen bonding/n−σ* overlap), ethylene, 1,3-butadiene, and benzene (π molecular orbitals), Re2Cl82–, and U2(COT)2 (metal–metal quadruple bonds). Transition state models illustrate orbital interactions in the SN2 reaction of cyanide with methyl, ethyl, and isopropyl chloride and in a hydroboration reaction of BH3 with propene. Composite EDS models of methyl and isopropyl chloride (for exploring their relative reactivities as SN2 electrophiles) and methylcyclohexane (visualizing 1,3-diaxial interactions) are described. Student perceptions of a multicolor 3D orbital print used in an introductory organic chemistry laboratory course are reported.

Force Decomposition Analysis: A Method to Decompose Intermolecular Forces into Physically Relevant Component Contributions

Computational quantum chemistry can be more than just numerical experiments when methods are specifically adapted to investigate chemical concepts. One important example is the development of energy decomposition analysis (EDA) to reveal the physical driving forces behind intermolecular interactions. In EDA, typically the interaction energy from a good-quality density functional theory (DFT) calculation is decomposed into multiple additive components that unveil permanent and induced electrostatics, Pauli repulsion, dispersion, and charge-transfer contributions to noncovalent interactions. Herein, we formulate, implement, and investigate decomposing the forces associated with intermolecular interactions into the same components. The resulting force decomposition analysis (FDA) is potentially useful as a complement to the EDA to understand chemistry, while also providing far more information than an EDA for data analysis purposes such as training physics-based force fields. We apply the FDA based on absolutely localized molecular orbitals (ALMOs) to analyze interactions of water with sodium and chloride ions as well as in the water dimer. We also analyze the forces responsible for geometric changes in carbon dioxide upon adsorption onto (and activation by) gold and silver anions. We also investigate how the force components of an EDA-based force field for water clusters, namely MB-UCB, compare to those from force decomposition analysis.

Theoretical exploration of new particle formation from glycol aldehyde in the atmosphere – A temperature-dependent study

Catalytic routes for the hydration and ammonolysis reactions of glycolaldehyde (OHCH2CHO), a bifunctional carbonyl compound in the atmosphere, is investigated employing density functional methods. Energetics of reactions catalysed by water (monomer and dimer), ammonia, and ammonia-water complex have been explored. A substantial lowering of activation energies has been noticed in all these assisted pathways compared to the unassisted mechanism. Transition state theory estimates reveal larger effective rate constants for the water-assisted pathways (for both hydration and ammonolysis) than other catalytic agents.The structural and thermodynamic properties of the molecular clusters have been investigated in the gas phase. Thermodynamic data reveals the exothermic formation of clusters. Important role of hydrogen bonding network towards stabilising the molecular clusters was noticed. This study may shed light on the underlying molecular insights on new particle formation from degradation products of glycol aldehyde under atmospheric conditions.

Development of accurate potentials for the physisorption of water on graphene.

From coupled-cluster singles and doubles model including connected triples corrections [CCSD(T)] calculations on the water dimer and B97D/CC on the water-circumcoronene complex at a large number of randomly generated conformations, interaction potentials for the physisorption of water on graphene are built, accomplishing almost sub-chemical accuracy. The force fields were constructed by decomposing the interaction into electrostatic and van der Waals contributions, the latter represented through improved Lennard-Jones potentials. Besides, a Chemistry at Harvard Macromolecular Mechanics (CHARMM)-like term was included in the water-water potential to improve the description of hydrogen bonds, and an induction term was added to model the polarization effects in the interaction between water and polyaromatic hydrocarbons (PAHs) or graphene. Two schemes with three and six point charges were considered for the interactions water-water and water-PAH, as Coulomb contributions are zero in the water-graphene system. The proposed fitted potentials reproduce the ab initio data used to build them in the whole range of distances and conformations and provide results for selected points very close to CCSD(T) benchmarks. When applied to the water-graphene system, the obtained results are in excellent agreement with p-CCSD(T), revised symmetry-adapted perturbation theory based on density functional theory monomer properties (DFT-SAPT), and diffusion Monte Carlo reference values. Furthermore, the stability of the various conformers water-PAH and water-graphene, as well as the different trends observed between these systems are rationalized in terms of the modifications of the electrostatic contribution.

Aggregation patterns of curcumin and piperine mixtures in different polar media.

This work reports a thorough molecular dynamics investigation on the aggregation patterns of curcumin and piperine in water, ethanol and a mixture of both solvents. The low solubility of curcumin in water results in a rapid formation of very stable dimers for both keto and enol tautomers. In agreement with a higher solubility, piperine molecules move closer and farther apart several times during the simulation, which indicates the formation of a less stable dimer in water. In contrast, both curcumin and piperine are soluble in ethanol and, thus, dimers can hardly be formed in this media. In comparison with a pure-water solvent, a 30 : 70 mixture of ethanol and water significantly reduces the probability of formation of most dimers of curcumin and piperine molecules. The simulations show that larger clusters may be complex structures, but the formation of stacks (in the case of piperine and enol tautomer of curcumin) and cages (when the keto tautomer of curcumin is involved) are not rare. Furthermore, it is shown that each single molecule presents a certain degree of mobility in the cluster, especially on the surface, but without leading to dissociation.

Controlling aromatic helix dimerization in water by tuning charge repulsions.

Several helically folded aromatic oligoamides were designed and synthesized. The sequences were all water-soluble thanks to the charged side chains borne by the monomers. Replacing a few, sometimes only two, charged side chains by neutral methoxy groups was shown to trigger the formation of various aggregates which could be tentatively assigned to head-to-head stacked dimers of single helices, double helical duplexes and a quadruplex, none of which would form in organic solvent with organic-soluble analogues. The nature of the aggregates was supported by concentration and solvent dependent NMR studies, 1H DOSY experiments, mass spectrometry, and X-ray crystallography or energy-minimized models, as well as analogies with earlier studies. The hydrophobic effect appears to be the main driving force for aggregation but it can be finely modulated by the presence or absence of a small number of charges to an extent that had no precedent in aromatic foldamer architectures. These results will serve as a benchmark for future foldamer design in water.

A possible atmospheric source of HNO3: the ammonolysis reaction of t-N2O4 in the presence of water monomer, water dimer, and sulfuric acid

The effort of water monomer, water dimer, and sulfuric acid on the ammonolysis of t-N2O4 were studied by quantum chemical method and the Master equation rate calculations.

Absorption by water dimers in the water vapor IR spectra at different temperatures

Absorption by water dimers in the water vapor IR spectra at different temperatures

MP2 study of the adsorption of CO2 onto the water monomer, dimer and trimer

MP2 study of the adsorption of CO2 onto the water monomer, dimer and trimer

Photochemistry of Thymine in Solution and DNA Revealed by an Electrostatic Embedding QM/MM Combined with Mixed-Reference Spin-Flip TDDFT

The photochemistry of nucleobases, important for their role as building blocks of DNA, is largely affected by the electrostatic environment in which they are soaked. For example, despite the numerous studies of thymine in solution and DNA, there is still a debate on the photochemical deactivation pathways after UV absorption. Many theoretical models are oversimplified due to the lack of computationally accurate and efficient electronic structure methodologies that capture excited state electron correlation effects when nucleobases are embedded in large electrostatic media. Here, we combine mixed-reference spin-flip time-dependent density functional theory (MRSF-TDDFT) with electrostatic embedding QM/MM using electrostatic potential fittingfitted (ESPF) atomic charges, as a strategy to accurately and efficiently describe the electronic structure of chromophores polarized by an electrostatic medium. In particular, we develop analytic expressions for the energy and gradient of MRSF/MM based on the ESPF coupling using atom-centered grids and total charge conservation. We apply this methodology to the study of solvation effects on thymine photochemistry in water and thymine dimers in DNA. In the former, the combination of trajectory surface hopping (TSH) nonadiabatic molecular dynamics (NAMD) with MRSF/MM remarkably revealed accelerated deactivation decay pathways, which is consistent with the experimental decay time of ∼400 fs. The enhanced hopping rate can be explained by the preferential stabilization of corresponding conical interactions due to their increased dipole moments. Structurally, it is a consequence of characteristic methyl puckered geometries near the conical intersection region. For the thymine dimer in B-DNA, we found new photochemical pathways through conical intersections that could explain the formation of cyclobutadiene dimers and 6-4 photoproducts.

Tracking water dimers in ambient nanocapsules by vibrational spectroscopy

Nanoconfined few-molecule water clusters are invaluable systems to study fundamental aspects of hydrogen bonding. Unfortunately, most experiments on water clusters must be performed at cryogenic temperatures. Probing water clusters in noncryogenic systems is however crucial to understand the behavior of confined water in atmospheric or biological settings, but such systems usually require either complex synthesis and/or introduce many confounding external bonds to the clusters. Here, we show that combining Raman spectroscopy with the molecular nanocapsule cucurbituril is a powerful technique to sequester and analyze water clusters in ambient conditions. We observe sharp peaks in vibrational spectra arising from a single rigid confined water dimer. The high resolution and rich information in these vibrational spectra allow us to track specific isotopic exchanges inside the water dimer, verified with density-functional theory and kinetic population modeling. We showcase the versatility of such molecular nanocapsules by tracking water cluster vibrations through systematic changes in confinement size, in temperatures up to 120° C, and in their chemical environment.

Water Dimer-Driven DNA Base Superstructure with Mismatched Hydrogen Bonding.

The existence of water dimers in equilibrium water vapor at room temperature and their anomalous properties revealed by recent studies suggest the benchmark role of water dimers in both experiment and theory. However, there has been a limited observation of individual water dimers due to the challenge of water separation and generation at the single-molecule level. Here, we achieve real-space imaging of individual confined water dimers embedded inside a self-assembled layer of a DNA base, adenine, on Ag(111). The hydration of the adenine layers by these water dimers causes a local surface chiral inversion in such a way that the neighboring homochiral adenine molecules become heterochiral after hydration, resulting in a mismatched hydrogen-bond pattern between neighboring adenine molecules. Furthermore, the mutual influence between the adenine superstructure and these dynamic confined water dimers is corroborated by theoretical simulation and calculations. The observation of single confined water dimers offers an unprecedented approach to studying the fundamental forms of water clusters and their interaction with the local chemical environment.

Research of Water Molecules Cluster Structuring during Haberlea rhodopensis Friv. Hydration

Gesneriaceae plant family is comprised of resurrection species, namely Boea hygrometrica and Paraboea rufescens, that are native to the Southeast Asia and Haberlea rhodopensis, Ramonda myconi, and Ramonda serbica, which are mainly found in the Balkan Peninsula. Haberlea rhodopensis is known to be able to survive extreme and prolonged dehydration. Study was carried out after the dried plant Haberlea rhodopensis Friv. had been hydrated and had reached its fresh state. Two juice samples were collected from the plant blossom: The first sample was prepared with 1% filtered water through a patented EVOdrop device. Then the sample was saturated with hydrogen with EVOdrop booster to a concentration of 1.2 ppm, pH = 7.3, ORP = −390 mV. This first sample was prepared with filtered tap water from Sofia, Bulgaria. The second sample, which was a control one, was developed with tap water from Sofia, Bulgaria, consisting of 1% solutions of Haberlea rhodopensis. A study revealed that during the drying process in H. rhodopensis the number of free water molecules decreases, and water dimers are formed. The aim of our study was to determine the number of water molecules in clusters in 1% solutions of hydrated H. rhodopensis plants. Results were analyzed according to the two types of water used in the experiment. Th EVOdrop device is equipped with an ultranano membrane and rotating jet nozzle to create a vortex water and saturation thanks to a second device EVObooster to obtain hydrogen-rich water. In the current study Hydrogen-rich water is referred to as Hydrogen EVOdrop Water (HEW). Research was conducted using the following methods—spectral methods non-equilibrium energy spectrum (NES) and differential non-equilibrium energy spectrum (DNES), mathematical models, and study of the distribution of water molecules in water clusters. In a licensed Eurotest Laboratory, the research of tap water before and after flowing through the EVOdrop device was proven. Studies have been carried out on the structuring of water molecule clusters after change of hydrogen bond energies. The restructuring comes with rearrangement of water molecules by the energy levels of hydrogen bonds. Local extrema can be observed in the spectrum with largest amount of water molecules. The structural changes were tested using the NES and DNES spectral methods. The conducted research proved that the application of EVOdrop device and EVObooster changes the parameters of water to benefit hydration and health.

Simultaneous and Spontaneous Oxidation and Reduction in Microdroplets by the Water Radical Cation/Anion Pair

AbstractMicrodroplets show unique chemistry, especially in their intrinsic redox properties, and to this we here add a case of simultaneous and spontaneous oxidation and reduction. We report the concurrent conversions of several phosphonates to phosphonic acids by reduction (R−P → H−P) and to pentavalent phosphoric acids by oxidation. The experimental results suggest that the active reagent is the water radical cation/anion pair. The water radical cation is observed directly as the ionized water dimer while the water radical anion is only seen indirectly though the spontaneous reduction of carbon dioxide to formate. The coexistence of oxidative and reductive species in turn supports the proposal of a double‐layer structure at the microdroplet surface, where the water radical cation and radical anion are separated and accumulated.