Large Clusters Of Water Molecules Research Articles

A Linear-Scaling Method for Noncovalent Interactions: An Efficient Combination of Absolutely Localized Molecular Orbitals and a Local Random Phase Approximation Approach.

A novel method for the accurate and efficient calculation of interaction energies in weakly bound complexes composed of a large number of molecules is presented. The new ALMO+RPAd method circumvents the prohibitive scaling of coupled cluster singles and doubles while still providing similar accuracy across a diverse range of weakly bound chemical systems. Linear-scaling procedures for the Fock build are given utilizing absolutely localized molecular orbitals (ALMOs), resulting in the a priori exclusion of basis set superposition errors. A bespoke data structure and algorithm using density fitting are described, leading to linear scaling for the storage and computation of the two-electron integrals. Electron correlation is included through a new, linear-scaling pairwise local random phase approximation approach, including exchange interactions, and decomposed into purely dispersive excitations (RPAxd). Collectively, these allow meaningful decomposition of the interaction energy into physically distinct contributions: electrostatic, polarization, charge transfer, and dispersion. Comparison with symmetry-adapted perturbation theory shows good qualitative agreement. Tests on various dimers and the S66 benchmark set demonstrate results within 0.5 kcal mol-1 of coupled cluster singles and doubles results. On a large cluster of water molecules, we achieve calculations involving over 3500 orbital and 12,000 auxiliary basis functions in under 10 min on a single CPU core.

The accuracy of ab initio calculations without ab initio calculations for charged systems: Kriging predictions of atomistic properties for ions in aqueous solutions.

Using the machine learning method kriging, we predict the energies of atoms in ion-water clusters, consisting of either Cl- or Na+ surrounded by a number of water molecules (i.e., without Na+Cl- interaction). These atomic energies are calculated following the topological energy partitioning method called Interacting Quantum Atoms (IQAs). Kriging predicts atomic properties (in this case IQA energies) by a model that has been trained over a small set of geometries with known property values. The results presented here are part of the development of an advanced type of force field, called FFLUX, which offers quantum mechanical information to molecular dynamics simulations without the limiting computational cost of ab initio calculations. The results reported for the prediction of the IQA components of the energy in the test set exhibit an accuracy of a few kJ/mol, corresponding to an average error of less than 5%, even when a large cluster of water molecules surrounding an ion is considered. Ions represent an important chemical system and this work shows that they can be correctly taken into account in the framework of the FFLUX force field.

Bioceramic Resonance Effect on Meridian Channels: A Pilot Study.

Bioceramic is a kind of material which emits nonionizing radiation and luminescence, induced by visible light. Bioceramic also facilitates the breakup of large clusters of water molecules by weakening hydrogen bonds. Hydrogen bond weakening, which allows water molecules to act in diverse ways under different conditions, is one of the key mechanisms underlying the effects of Bioceramic on biophysical and physical-chemical processes. Herein, we used sound to amplify the effect of Bioceramic and further developed an experimental device for use in humans. Thirteen patients who suffered from various chronic and acute illnesses that severely affected their sleep patterns and life quality were enrolled in a trial of Bioceramic resonance (i.e., rhythmic 100-dB sound waves with frequency set at 10 Hz) applied to the skin surface of the anterior chest. According to preliminary data, a “Propagated Sensation along Meridians” (PSM) was experienced in all Bioceramic resonance-treated patients but not in any of the nine control patients. The device was believed to enhance microcirculation through a series of biomolecular and physiological processes and to subject the specific meridian channels of Traditional Chinese Medicine (TCM) to coherent vibration. This noninvasive technique may offer an alternative to needle acupuncture and other traditional medical practices with clinical benefits.

Hydrogen bonding patterns in different acrylamide–water clusters: microsolvation probed by micro Raman spectroscopy and DFT calculations

We report in this study on the hydrogen bonding patterns between acrylamide (Acr) and water (W) as a H-donor. Hydrogen bonds between Acr and water molecules and among different water molecules significantly influence the spectral features. Raman spectra of neat Acr and its mixtures with water were recorded in the region, 1800–400 cm−1. A careful analysis of the spectra reveals that upon dilution, the additional peaks are observed at 831 and 1124 cm−1, ∼10 and ∼18 cm−1 away from the main bands at ∼842 and ∼1142 cm−1, respectively, which were attributed to the hydrogen bonding of Acr with water. The new band at ∼1083 cm−1 clearly reveals a nice example of the increment on the degree of hydrogen bonding in terms of multiple hydrogen bonded molecules. The temperature dependent Raman spectra of Acr at nine different temperatures were also recorded, and a significant change in spectral features observed at ∼373 K is attributed to crystal → liquid transition. A new peak at 1620 cm−1 appears to be due to a change in the symmetry of self associated Acr (dimer and trimer) molecules at 373 K. DFT calculations were performed using B3LYP/6-311++G(d,p) to obtain the ground state optimized geometries of neat, self associated dimeric and trimeric forms, and hydrogen bonded complexes in gas phase. The DFT computations were also performed on various (Acr + Wn, n = 1–15) clusters in order to explore the microsolvation. A broad configuration search was performed to identify the lowest energy clusters of Acr with varying number of water molecules. The structures of the clusters are analyzed in terms of the hydrogen bonding network established among the water molecules and between Acr and water molecules. Overall the present study gives a clue regarding the stabilization of the Acr molecule in a large cluster of water molecules.

UV resonance Raman determination of molecular mechanism of poly(N-isopropylacrylamide) volume phase transition.

Poly(N-isopropylacrylamide) (PNIPAM) is the premier example of a macromolecule that undergoes a hydrophobic collapse when heated above its lower critical solution temperature (LCST). Here we utilize dynamic light scattering, H-NMR, and steady-state and time-resolved UVRR measurements to determine the molecular mechanism of PNIPAM's hydrophobic collapse. Our steady-state results indicate that in the collapsed state the amide bonds of PNIPAM do not engage in interamide hydrogen bonding, but are hydrogen bonded to water molecules. At low temperatures, the amide bonds of PNIPAM are predominantly fully water hydrogen bonded, whereas, in the collapsed state one of the two normal CO hydrogen bonds is lost. The NH-water hydrogen bonding, however, remains unperturbed by the PNIPAM collapse. Our kinetic results indicate a monoexponential collapse with tau approximately 360 (+/-85) ns. The collapse rate indicates a persistence length of n approximately 10. At lengths shorter than the persistence length the polymer acts as an elastic rod, whereas at lengths longer than the persistence length the polymer backbone conformation forms a random coil. On the basis of these results, we propose the following mechanism for the PNIPAM volume phase transition. At low temperatures PNIPAM adopts an extended, water-exposed conformation that is stabilized by favorable NIPAM-water solvation shell interactions which stabilize large clusters of water molecules. As the temperature increases an increasing entropic penalty occurs for the water molecules situated at the surface of the hydrophobic isopropyl groups. A cooperative transition occurs where hydrophobic collapse minimizes the exposed hydrophobic surface area. The polymer structural change forces the amide carbonyl and N-H to invaginate and the water clusters cease to be stabilized and are expelled. In this compact state, PNIPAM forms small hydrophobic nanopockets where the (i, i + 3) isopropyl groups make hydrophobic contacts. A persistent length of n approximately 10 suggests a cooperative collapse where hydrophobic interactions between adjacent hydrophobic pockets stabilize the collapsed PNIPAM.

Large heat capacity change in a protein-monovalent cation interaction.

Current views about protein-ligand interactions state that electrostatic forces drive the binding of charged species and that burial of hydrophobic and polar surfaces controls the heat capacity change associated with the reaction. For the interaction of a protein with a monovalent cation the electrostatic components are expected to be significant due to the ionic nature of the ligand, whereas the heat capacity change is expected to be small due to the size of the surface area involved in the recognition event. The physiologically important interaction of Na+ with thrombin was studied over the temperature range from 5 to 45 degrees C and the ionic strength range from 50 to 800 mM. These measurements reveal an unanticipated result that bears quite generally on studies of molecular recognition and protein folding. Binding of Na+ to thrombin is characterized by a modest dependence on ionic strength but a large and negative heat capacity change of -1.1 +/- 0.1 kcal mol-1 K-1. The small electrostatic coupling can be explained in terms of a minimal perturbation of the ionic atmosphere of the protein upon Na+ binding. The large heat capacity change, however, is difficult to reconcile with current views on the origin of this effect from surface area changes or large folding transitions coupled to binding. It is proposed that this change is linked to burial of a large cluster of water molecules in the Na+ binding pocket upon Na+ binding. Due to their reduced mobility and highly ordered structure, water molecules sequestered in the interior of a protein must have a lower heat capacity compared to those on the surface of a protein or in the bulk solvent. Hence, a binding or folding event where water molecules are buried may result in significant heat capacity changes independent of changes in exposed hydrophobic surface or coupled conformational transitions.

Hydrogen bonding in long chains of hydrogen fluoride and long chains and large clusters of water molecules

Energy band structures of one-dimensional (HF)n- and (H2O)n-chains have been calculated (1) by extrapolation of CNDO/2-MO levels to infinite chain length and (2) by the CNDO/2 crystal orbital (CO) method. In the CO-calculations interactions up to fifth neighbours have been taken into account. Both types of calculations were performed using experimental geometries and CNDO/2 minimum geometries of the corresponding dimers (HF)2 and (H2O)2. With the same geometries CO calculations on two-dimensional sheets of hydrogen bonded chains were performed too.