Adding Water Molecules Research Articles

Computational study of carbon monooxide absorption by ultradisperse systems. Emission spectra

Molecular dynamics was used to study absorption of carbon monoxide molecules by water clusters combined into two groups (2–10 and 11–20 water molecules) on the basis of their statistical weights. Spectral characteristics of the clusters in the frequency range 0 ≤ ω ≤ 1000 cm−1 were established. Within this range, the integral IR adsorption intensity of both systems increases with addition of CO molecules. The IR emission power increases significantly after a cluster has absorbed one CO molecule but decreases with the absorption of a further CO molecule. A similar situation is observed with the number of electrons “active” toward external electromagnetic radiation. As the smallest clusters containing two CO molecules grow by adding water molecules, the IR emission power decreases. In other cases, these changes are of a periodical character.

Density functional theory studies of model complexes for molybdenum-dependent nitrate reductase active sites

Molybdenum and tungsten complexes as models for the active sites of assimilatory or dissimilatory nitrate reductases (NR) were computed at the CPCM-B98/SDDp//B3LYP/Lanl2DZp* plus zero point energy level of density functional theory. The ligands were chosen on the basis of available experimental protein or small chemical model structures. A water molecule is found to bind to assimilatory NR models [(Me(2)C(2)S(2))MO(YMe)](-) (-11.5 kcal mol(-1) for M is Mo, Y is S) and may be replaced by nitrate (-4.5 kcal mol(-1)) (but a hydroxy group may not). Nature's choice of M is Mo and Y is S for NR has the largest activation energy for protein-free models (13.3 kcal mol(-1)) and the least exothermic reaction energy for the nitrate reduction (-14.9 kcal mol(-1)) compared with M is W and Y is O or Se alternatives. Water binding to dissimilatory NR model complexes [(Me(2)C(2)S(2))(2)M(YR)](-) is considerably endothermic (10.3 kcal mol(-1)); nitrate binding is only slightly so (1.5 kcal mol(-1) for RY(-) is MeS(-)). The exchange of an oxo ligand (assimilatory NR) for a dithiolato ligand (dissimilatory NR model) reduces the exothermicity (-8.6 kcal mol(-1) relative to the fivefold-coordinate reduced complex) and raises the barrier for oxygen atom transfer (OAT) in the nitrate complex (19.2 kcal mol(-1)). Not for the mono but only for the bisdithiolato complexes hydrogen bonding involving the coordinated substrate may significantly lower the OAT barrier as shown by explicitly adding water molecules. Substitution of tungsten for molybdenum generally lowers OAT activation energies and makes nitrate reduction reaction energies more negative. Bidentate carboxylato binding identified in Escherichia coli NarGHI is the preferred binding mode also for an acetato model. However, one dithiolato ligand folds when the Mo(VI) center is bare of a good pi-donor ligand, e.g., an oxo group. Computations on [(mnt)(2)Mo(IV)(YR)(PPh(3))](-) [mnt is (CN)(2)C(2)S(2) (2-)] gave a smaller nitrate reduction activation energy for RY(-) is Cl(-), compared with RY(-) is PhS(-), although experimentally only the phenyl thiolato complex and not the chloro complex was found to be a functional NR model.

Theoretical studies on the reaction of pentafulvenone with water in gas phase and aqueous solvent

In gas phase, the hydrations of pentafulvenone to generate three types of cyclopentadienyl carboxylic acids are studied theoretically at the MP2/6-311+G**//B3LYP/6-311+G** level. A water molecule attacking the C=O double bond of pentafulvenone can yield cyclopentadienyl carboxylic acids via the formation of fulvenediols, and attacking the C=C double bond of pentafulvenone can directly yield cyclopentadienyl carboxylic acid. The barriers of rate-determining transition states are 42.2 and 30.4 kcal mol−1, respectively. The barriers of rate-determining transition states for two water molecules system are 20.2 and 19.6 kcal mol−1, respectively. The products can isomerize to each other. In aqueous solvent, the hydrations of pentafulvenone are investigated using PCM-UAHF model at the MP2 (PCM)/6-311+G**// B3LYP (PCM)/6-311+G** and MP2 (PCM)/6-311+G**// B3LYP/6-311+G** levels. The barriers of all rate-determining transition states are decreased. The added water molecule acts as catalyst in both gas phase and aqueous solvent.

The Effect of Water on the Microstructure of 1‐Butyl‐3‐methylimidazolium Tetrafluoroborate/TX‐100/Benzene Ionic Liquid Microemulsions

The ionic liquid (IL) 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF4]) forms nonaqueous microemulsions with benzene with the aid of nonionic surfactant TX-100. The phase diagram of the ternary system was prepared, and the microstructures of the microemulsion were recognized. On the basis of the phase diagram, a series of ionic liquid-in-oil (IL/O) microemulsions were chosen and characterized by dynamic light scattering (DLS), which shows a similar swelling behavior to typical water-in-oil (W/O) microemulsions. The existence of IL pools in the IL/O microemulsion was confirmed by UV/Vis spectroscopic analysis with CoCl2 and methylene blue (MB) as the absorption probes. A constant polarity of the IL pool is observed, even if small amounts of water are added to the microemulsion, thus suggesting that the water molecules are solubilized in the polar outer shell of the microemulsion, as confirmed by FTIR spectra. 1H NMR spectroscopic analysis shows that these water molecules interact with the electronegative oxygen atoms of the oxyethylene (OE) units of TX-100 through hydrogen-bonding interactions, and the electronegative oxygen atoms of the water molecules attract the electropositive imidazolium rings of [bmim][BF4]. Hence, the water molecules are like a glue that stick the IL and OE units more tightly together and thus make the microemulsion system more stable. Considering the unique solubilization behavior of added water molecules, the IL/O microemulsion system may be used as a medium to prepare porous or hollow nanomaterials by hydrolysis reactions.

Role of Solubilized Water in the Reverse Ionic Liquid Microemulsion of 1-Butyl-3-methylimidazolium Tetrafluoroborate/TX-100/Benzene

The ionic liquid (IL) 1-butyl-3-methylimidazolium tetrafluoroborate (bmimBF4) can form nonaqueous microemulsions with benzene by the aid of nonionic surfactant TX-100. The effect of water on ionic liquid-in-oil (IL/O) microemulsions was studied, and it was shown that the addition of small amount of water to the IL microemulsion contributed to the stability of microemulsion and thus increased the amount of solubilized bmimBF4 in the microemulsion. The conductivity measurements also showed that the attractive interactions between IL microdroplets were weakened, that is, the IL/O microemulsion becomes more stable in the present of some water. Fourier transform IR was carried out to analyze the states of the added water, and the result showed that these water molecules mainly behaved as bound water and trapped water, indicating that the water molecules are located in the palisade layers of the IL/O microemulsion. Furthermore, 1H NMR and 19F NMR spectra suggested that the added water molecules built the hydrogen binding network of imidazolium cations and H2O, BF4- anion and H2O, and at the same time the electronegative oxygen atoms of the oxyethylene units of TX-100 and water in the palisade layers, which made the palisade layers more firm and thus increased the stability of the microemulsion. The study can help in further understanding the formation mechanism of microemulsions. In addition, the characteristic solubilization behavior of the added water can provide an aqueous interface film for hydrolysis reactions and therefore may be used as an ideal medium to prepare porous or hollow nanomaterials.

Exploration of the Ca2+ Interaction Modes of the Nifedipine Calcium Channel Antagonist

A comprehensive study is carried out using quantum chemical computation and molecular dynamics (MD) simulations to gain insight into the interaction between Ca(2+) ions and the most important class of calcium channel antagonists--nifedipine. First, the chelating structures and energetic characters of nifedipine-Ca(2+) in the gas phase are explored, and 25 isomers are found. The most favorable chelating mode is a tridentate one, that is, Ca(2+) binds to two carbonyl O atoms and one nitryl O atom, where Ca(2+) is above the plane of the three O atoms to form a pyramidal structure. Accurate geometric structures, relative stabilities, vertical and adiabatic binding energies, and charge distributions are discussed. The differences in the geometries and energies among these isomers are analyzed from the contributions of chelating sites, electrostatics and polarizations, steric repulsions, and charge distributions. The interconversions among isomers with similar geometries and energies are also investigated because of the importance of the geometric transformation in the biological system. Furthermore, certain numbers of water molecules are added to the nifedipine-Ca(2+) system to probe the effect of water. A detailed study is performed on the hydrated geometries on the basis of the most stable isomer 1. Stepwise hydration can weaken the nifedipine-Ca(2+) interaction, and the chelating sites of nifedipine are gradually replaced by the added water molecules. Hexacoordination is found to be the most favorable geometry no matter how many water molecules were added, which can be verified by the MD simulations. The transfer of water molecules from the inner shell to the outer shell is also supported by MD simulations of the hexahydrated complexes.

Hydration effect on interaction mode between glutamic acid and Ca2+ and its biochemical implication: a theoretical exploration

The stepwise hydration effect on the glutamic acid–Ca2+ (GC) complexes in the gas phase has been investigated by density functional theory (DFT) calculations. The thermodynamics parameters for the hydration reactions, the stepwise hydration energies and accurate geometries have been explored. To elucidate the Ca2+–ligand interaction, the charge transfer, bonding analysis and IR spectroscopic characteristics have also been investigated. The correlating data have shown that all of the stepwise hydration reactions are enthalpy-driven because of the relatively small value of ΔS, but the number of coordinated water molecules in the first shell of Ca2+ is not limitless. In our study, the optimal coordination number (CN) of Ca2+ in the first shell is 6 or 7; the former value agrees well with the data reported in the Protein Data Bank (PDB), and the latter is the reflection of the most frequent Ca2+-binding motif, EF-hand, in soluble proteins. Furthermore, the self-consistent reaction field (SCRF) and higher-level MP2 calculations have confirmed our conclusions. Additionally and very importantly, the stepwise hydration in either the first or second coordination shell can weaken the glutamic acid–Ca2+ interaction gradually till the glutamic acid ligand is replaced by the added water molecules, resulting in the conversion of coordination mode of the glutamic acid to Ca2+ from the inner-sphere one to a peripheral interaction mode, just like the ligand exchange process in the Ca2+ release channel existing in the real biological system. Finally, the similarities and discrepancies between our model and the Ca2+-channel in vivo have been compared.

Ab Initio Study on Adsorption of Hydrated Na+ and Cu+ Cations on the Cu(111) Surface

The interactions of Na+ and Cu+ cations with a Cu(111) surface in the presence and absence of water molecules were investigated using cluster models and ab initio methods. Adsorption in aqueous solution was modeled with one to five water molecules around the adsorbing cation. The Cu surface was described with Cu10 and Cu18 cluster models and the computational method was MP2/RECP/6-31+G. The effect of the basis set superposition error (BSSE) was taken into account with counterpoise (CP) correction, and the accuracy of HF-level results was examined. The interactions between Na+ and the Cu surface were found to be primarily electrostatic, and the energy differences among the different adsorption sites were small. The largest CP-corrected MP2 adsorption energy for the Cu18 cluster was -188 kJ/mol. When water molecules were added around it, Na+ receded from the Cu surface and finally was surrounded totally by the water molecules. The interactions between Cu+ and the Cu surface were dominated by orbital interactions, and Cu+ preferred to adsorb on sites where it could bind to more than one surface atom. The largest CP-corrected MP2 adsorption energy for the Cu18 cluster was -447 kJ/mol. Adding water molecules around it did not cause Cu+ to draw away from the surface, but instead the water molecules began to form hydrogen bonds with one another. The magnitude of BSSE was substantial in most cases. CP corrections did not, however, have a significant impact on the relative trends among the interaction energies.

Hydrogen bonding, solvation, and hydrolysis of cisplatin: a theoretical study.

Density functional calculations on a range of hydrogen bonded clusters of cisplatin are reported. A systematic search of 1:1 cisplatin:water complexes reveals only three stable minima, which contain a number of common, recurring interactions, such as an N-H...O-H...Cl bridging mode. Expanding these clusters by adding water molecules leads to a model of the first solvation shell of cisplatin, which contains the above motifs along with several strong water-water interactions. The strengths of such interactions are rationalized on the basis of electrostatic potentials, and quantified by use of Atoms in Molecules properties. This analysis also allows us to estimate cisplatin's position on Abraham's hydrogen bond acidity and basicity scales, indicating that cisplatin is a strong donor and acceptor of hydrogen bonds due to the dominance of hard, electrostatic interactions. The effects of this explicit solvation on the barrier to hydrolysis, and hence activation, of cisplatin are explored, indicating a slightly higher barrier than in the gas phase, leading to better agreement with experiment than either gas phase or continuum solvation calculations.

Nature of One-Dimensional Short Hydrogen Bonding: Bond Distances, Bond Energies, and Solvent Effects

On the basis of recently synthesized calix[4]hydroquinone (CHQ) nanotubes which were self-assembled with infinitely long one-dimensional (1-D) short hydrogen bonds (SHB), we have investigated the nature of 1-D SHB using first-principles calculations for all the systems including the solvent water. The H-bonds relay (i.e., contiguous H-bonds) effect in CHQs shortens the H...O bond distances significantly (by more than 0.2 A) and increases the bond dissociation energy to a large extent (by more than approximately 4 kcal/mol) due to the highly enhanced polarization effect along the H-bond relay chain. The H-bonds relay effect shows a large increase in the chemical shift associated with the SHB. The average binding energies for the infinite 1-D H-bond arrays of dioles and dions increase by approximately 4 and approximately 9 kcal/mol per H-bond, respectively. The solvent effect (due to nonbridging water molecules) has been studied by explicitly adding water molecules in the CHQ tube crystals. This effect is found to be small with slight weakening of the SHB strength; the H...O bond distance increases only by 0.02 A, and the average binding energy decreases by approximately 1 kcal/mol per H-bond. All these results based on the first-principles calculations are the first detailed analysis of energy gain by SHB and energy loss by solvent effect, based on a partitioning scheme of the interaction energy components. These reliable results elucidate not only the self-assembly phenomena based on the H-bond relay but also the solvent effect on the SHB strength.

Chelate effect and thermodynamics of metal complex formation in solution: a quantum chemical study.

The accuracy of quantum chemical predictions of structures and thermodynamic data for metal complexes depends both on the quantum chemical methods and the chemical models used. A thermodynamic analogue of the Eigen-Wilkins mechanism for ligand substitution reactions (Model A) turns out to be sufficiently simple to catch the essential chemistry of complex formation reactions and allows quantum chemical calculations at the ab initio level of thermodynamic quantities both in gas phase and solution; the latter by using the conductor-like polarizable continuum (CPCM) model. Model A describes the complex formation as a two-step reaction: 1. [M(H2O)x](aq) + L(aq) <==>[M(H2O)x], L(aq); 2. [M(H2O)x], L(aq) <==>[M(H2O)(x-1)L],(H2O)(aq). The first step, the formation of an outer-sphere complex is described using the Fuoss equation and the second, the intramolecular exchange between an entering ligand from the second and water in the first coordination shell, using quantum chemical methods. The thermodynamic quantities for this model were compared to those for the reaction: [M(H2O)x](aq) + L(aq) <==>[M(H2O)(x-1)L](aq) + (H2O)(aq) (Model B), as calculated for each reactant and product separately. The models were tested using complex formation between Zn(2+) and ammonia, methylamine, and ethylenediamine, and complex formation and chelate ring closure reactions in binary and ternary UO(2)(2+)-oxalate systems. The results show that the Gibbs energy of reaction for Model A are not strongly dependent on the number of water ligands and the structure of the second coordination sphere; it provides a much more precise estimate of the thermodynamics of complex formation reactions in solution than that obtained from Model B. The agreement between the experimental and calculated data for the formation of Zn(NH(3))(2+)(aq) and Zn(NH(3))(2)(2+)(aq) is better than 8 kJ/mol for the former, as compared to 30 kJ/mol or larger, for the latter. The Gibbs energy of reaction obtained for the UO(2)(2+) oxalate systems using model B differs between 80 and 130 kJ/mol from the experimental results, whereas the agreement with Model A is better. The errors in the quantum chemical estimates of the entropy and enthalpy of reaction are somewhat larger than those for the Gibbs energy, but still in fair agreement with experiments; adding water molecules in the second coordination sphere improves the agreement significantly. Reasons for the different performance of the two models are discussed. The quantum chemical data were used to discuss the microscopic basis of experimental enthalpy and entropy data, to determine the enthalpy and entropy contributions in chelate ring closure reactions and to discuss the origin of the so-called "chelate effect". Contrary to many earlier suggestions, this is not even in the gas phase, a result of changes in translation entropy contributions. There is no simple explanation of the high stability of chelate complexes; it is a result of both enthalpy and entropy contributions that vary from one system to the other.

Reactivity of phosphate monoester monoanions in aqueous solution. 1. Quantum mechanical calculations support the existence of "anionic zwitterion" MeO(+)(H)PO(3)(2-) as a key intermediate in the dissociative hydrolysis of the methyl phosphate anion.

The dissociative hydrolysis reaction of the methyl phosphate monoanion has been studied for the reactant species CH(3)OPO(3)H(-) (1) and CH(3)OPO(3)H(-) x H(2)O (1a) in the gas and aqueous phases by density functional theory (B3LYP) calculations. Nonspecific solvation effects were taken into account with the polarizable continuum model PCM either by solvating the gas-phase reaction paths or by performing geometry searches directly in the presence of the solvation correction. In agreement with previous theoretical studies, our gas-phase calculations indicate that proton transfer to the methoxy group of 1 is concerted with P-O bond cleavage. In contrast, optimizations performed with the PCM solvation model establish the existence of the tautomeric form CH(3)O(+)(H)PO(3)(2-) (2) as an intermediate, indicating that proton transfer and P-O bond cleavage become uncoupled in aqueous solution. The dissociative pathway of 1a is energetically favored over the dissociative pathway of 1 only when the added water molecule plays an active catalytic role in the prototropic rearrangement 1 <--> 2. In that case, it is found that the collapse (via P-O bond cleavage) of the hydrated zwitterionic form CH(3)O(+)(H)PO(3)(2-) x H(2)O (2a) is rate-determining. This collapse may occur by a stepwise mechanism through a very short-lived metaphosphate intermediate (PO(3)(-)), or by a concerted S(N)2-like displacement through a loose metaphosphate-like transition state. The present calculations do not allow a distinction to be made between these two alternatives, which are both in excellent agreement with experiment. The present study also reveals that PO(3)(-) reacts selectively with CH(3)OH and H(2)O nucleophiles in aqueous solution. However, the observed selectivity of metaphosphate is governed by solvation effects, not nucleophilicity (water being much more effective than methanol in capturing PO(3)(-)). This arises from a better solvation of the addition product H(2)O(+)PO(3)(2-) as compared to CH(3)O(+)(H)PO(3)(2-).

Strontium tantalates with a perovskite structure : Their conductivity and high-temperature interaction with water

The interaction of perovskite-like solid solutions Sr6 – 2xTa2 + 2xO11 + 3x(x= 0–0.28) with water is studied, along with dependences of the solutions' conductivity on their composition and the atmosphere's temperature and humidity. The Sr6 – 2xTa2 + 2xO11 + 3xphases with high concentrations of structural oxygen vacancies are high-temperature mixed oxygen–hydrogen ionic conductors whose conduction is sensitive to the presence of water vapor up to 900°C. According to a thermogravimetric study, the amount of water incorporated into the complex-oxide matrix is proportional to the concentration of structural oxygen vacancies. The process of water incorporation is considered in terms of crystalline and chemical properties of the structure. The oxygen-deficient perovskites containing coordination-unsaturated metalatoms can reconstruct their coordination polyhedron by adding water molecules, with subsequent partial dissociation of water to hydroxyl groups. The proposed mechanism explains different states of water in the oxide and a two-stage nature of its removal: water molecules coordinating the metal atom and those surrounding OH–leave the core in the first and second stages, respectively.

L-Alanyl-L-alanine in the zwitterionic state: structures determined in the presence of explicit water molecules and with continuum models using density functional theory

Abstract The structures and relative energies for L-alanyl-L-alanine (LALA) in the presence of explicit water molecules have been determined by using the density functional theory (DFT) Becke3–Lee–Yang–Parr functional and the 6-31G* basis set (B3LYP/6-31G*). In aqueous solution the dominant state of LALA is the zwitterionic form, while its neutral form is dominant in vacuo. Attempts to locate or determine a gas-phase zwitterionic species failed. That is, on the B3LYP/6-31G* potential energy surface, there is no barrier to proton transfer from the positively charged ammonium group to the negatively charged carboxylate group, or from the ammonium group to the adjacent carbonyl oxygen and from the amide nitrogen to the carboxylate group. To stabilize the zwitterion, we modelled the system by adding explicit water molecules and by placing the zwitterion within a sphere surrounded by a medium with a dielectric constant of 78.5, that is, within the Onsager continuum model, where the recommended cavity radius is obtained from a solute volume calculation. The zwitterionic species is only stable in the presence of water at the B3LYP/6-31G* level. This makes it imperative to include water molecules to model the zwitterionic species of LALA, peptides and amino acids at the B3LYP/6-31G* level. Finally, the zwitterionic structure stabilized by explicit water molecules has also been modelled within the Onsager theory. Here the Onsager model represents the effects due to the bulk water and the explicit water molecules stand for the effect due to direct H-bonding between the zwitterion and the solvent, that is, the first solvation shell. We used molecular dynamics simulations utilizing the CHARMm force field to produce structural input for the subsequent quantum-mechanical simulations. The structures determined using various methods to model the LALA zwitterionic form in aqueous solution were compared. We were able to find additional stable structures for LALA by adding water molecules and optimizing it which could not be obtained by using the Onsager theory. This shows that one must be careful when using continuum models to study peptides and proteins or other methods which do not take into account the explicit interactions between the solute and the first solvent shell.

Viscosity and photon correlation spectroscopy measurements in aqueous solutions of poly(ethylene glycol)

Abstract The present work reports the results of viscosity and Photon Correlation Spectroscopy (PCS) measurements performed on polymeric aqueous solutions. The viscosity data show that the transport properties of the H2O molecules in the presence of poly(ethylene glycol) differ greatly from those in the bulk. PCS data, on the other hand, allow us to evaluate the mutual diffusion coefficient and show that in the dilute region the system behaves as a polymer in a good solvent, whereas, at higher concentration indicates a scale behaviour, in agreement with the De Gennes scaling model for semi diluted solutions in a good solvent. An interpretative picture is proposed from these data: starting from pure polymers, and adding water molecules a certain number of these bond by H-bonding to the oxygen atoms of the oxirane groups, each oxygen atom being able to tie two water molecules so that the water-polymer interaction (hydration) plays a major role in the transport properties.

N-Acetyl-L-alanine N′-methylamide: a density functional analysis of the vibrational absorption and vibrational circular dichroism spectra

Abstract Ab initio 6-31G∗ Becke 3LYP DFT optimized geometries, vibrational frequencies, vibrational absorption (VA) intensities and vibrational circular dichroism (VCD) intensities have been calculated for the eight low energy conformers of N-acetyl-L-alanine N′-methylamide (L-AANMA) in the gas phase and one conformer stabilized by the addition of four water molecules. The VA and VCD spectra are calculated with the 6-31G∗ Becke 3LYP force fields (Hessians) and atomic polar tensors (APT); 6-31G∗∗ RHF atomic axial tensors (AAT) for the eight gas phase structures and 6-31G∗/6-31G RHF AAT for the L-AANMA-water complex. The VA and VCD spectra are also calculated using the 6-31G∗ Becke 3LYP Hessians; 6-31G∗∗ RHF APT and AAT for the eight gas phase structures and 6-31G∗/6-31G RHF APT and AAT for the L-AANMA-water complex. The rotational strengths of the amide A, I, II, III, IV, V and VI modes found in proteins as a function of φ and ψ (for various secondary structures) are for the first time reported for an inherently optically active molecule (non-glycine model) using the 6-31G∗∗ and 6-31G∗/6-31G RHF DOG AAT and 6-31G∗ Becke 3LYP Hessians and APT. This is also the first reported VCD calculation of a molecule with the solvent present. The molecule is not completely solvated, but the important hydrogen-bonded interactions are present and the feasibility of the calculation of the Hessian, APT and AAT with solvent molecules present is demonstrated. The VA and VCD spectra are compared to the experimental VA and VCD spectra in the literature and the conformational analysis (CA) and vibrational assignment of L-AANMA are reinvestigated. The rotational strengths of the amide modes for the various conformers are also compared to peptide and protein VCD spectra of molecules with known secondary structures. The agreement between the calculated rotational strengths of the various amide modes for which experimental measurements have been made is very good, in particular, for the right handed α-helical conformation of a poly(L-amino acid) we correctly predict the negative couplet for the amide A band, the positive couplet for the amide I band and the negative monosignate signal for the amide II band as measured by the groups of Nafie and Keiderling. The large change in the amide I region in aqueous solution from this region in carbon tetrachloride or the Ar matrix is also reproduced, documenting that the qualitative features of the vibrational absorption and VCD spectra can reproduced by explicitly adding water molecules to the Hessian and tensor calculations.

A molecular orbital study of bonding and frequency shifts in free and solvated lithium thiocyanate aggregates

The MNDO method has been used to determine the stable structures of lithium thiocyanate aggregates. Two classes of aggregates have been found: (a) N-bonded (LiNCS) p (1 $ ̌ / p⩽ 4) (i.e. linear LiNCS), the rhombic dimer, the triangular trimer and a cubane-like tetramer; (b) (LiSCN) p aggregates (1 $ ̌ / p⩽ 3) with lithium bridges between S and C. The structures of class (a) are in agreement with those experimentally determined in solution; in this case unusual negative frequency shifts of ν(CN) due to μ 2 or gm 3 nitrogen coordination have been reproduced by our vibrational frequency calculations. IR intensity variations are also in qualitative agreement with experiment. The lithium solvation has been simulated by adding water molecules in the first solvation shell of Li in order to complete its coordination number to 4. This model gives a good account of aggregation energies in solution and of ν(CN) frequency variations.

The structural variation and probability redistribution in alanine dipeptide conformers by hydration

The effects on structural variation and relative stability caused by hydration of alanine dipeptide in the C eq 7, C ax 7, C 5, α R and P II conformations were investigated by the method of the SUMSL (secant-type unconstrained minimization solver) energy-minimization technique, using the empirical potential energy function of the solute and the ST2 water model. The binding sites of water molecules in the solute were selected from spherical interaction energy maps. As a function of the number of added water molecules, we traced the structural variations mainly in the (ø,ψ) torsion angle space, and calculated the total internal energies of each solute-water system to evaluate the relative probabilities between those five conformers. The results indicate that the conformers having no intramolecular hydrogen bonds, such as α R, C 5 and P II, show larger structural variations than the C ax 7 and C eq 7 conformers which have intramolecular hydrogen bonds. The torsion angle, ψ, fluctuated more than ø for all the examined conformers. The energetically dominant conformation is shifted from C eq 7 to α R as the hydration progresses.

Collective vibrations of an alpha-helix. A molecular dynamics study

The internal dynamics of a 20-residue polyalanine helix was investigated by molecular dynamics simulations. Special attention was paid to the collective vibrations of the helix backbone. The stretch and bend vibrations could be assigned unambiguously to oscillations with periods of 1.4 and 4.3 ps, respectively. The influence of the environment on the dynamics of the collective vibrations was studied by coupling the helix to a heat bath and by adding water molecules. In the presence of water, the stretch vibration becomes more strongly dampened, but still exists as a vibration , while the bend vibration becomes overdamped and degenerates into a relaxation process. The results are compared with available experimental data.

Heterocyclic studies—XXX: Application of mass spectrometry to the study of covalent hydration

AbstractComparison of the mass spectra of 3,4‐hydrated 4‐trifluoromethylpteridine derivatives with those of corresponding anhydrous compounds shows that this technique can be used to deduce the position of covalent hydration in heterocyclic compounds.It is less easy to demonstrate the presence of added water molecules in 5,6,7,8‐dihydrated derivatives of ethyl pteridine‐4‐carboxylates, but spectra run at low ionising voltages give the required information.Two hydrates (3,4‐hydrates of 4‐ethoxycarbonyl‐ and 4‐trifluoromethyl‐pteridine‐2(1H)‐thione) which are very much more thermally stable than usual are also discussed.Metastable peaks and accurate mass measurements support many of the postulated fragmentation pathways.