Extracting elements of molecular structure from the all-particle wave function

Structural information is extracted from the all-particle (non-Born-Oppenheimer) wave function by calculating radial and angular densities derived from n-particle densities. As a result, one- and two-dimensional motifs of classical molecular structure can be recognized in quantum mechanics. Numerical examples are presented for three- (H(-), Ps(-), H(2)(+)), four- (Ps(2), H(2)), and five-particle (H(2)D(+)) systems.     

Infrared and vibrational CD spectra of partially solvated alpha-helices: DFT-based simulations with explicit solvent

Theoretical simulations are used to investigate the effects of aqueous solvent on the vibrational spectra of model alpha-helices, which are only partly exposed to solvent to mimic alpha-helices in proteins. Infrared absorption (IR) and vibrational circular dichroism (VCD) amide I' spectra for 15-amide alanine alpha-helices are simulated using density functional theory (DFT) calculations combined with the property transfer method. The solvent is modeled by explicit water molecules hydrogen bonded to the solvated amide groups. Simulated spectra for two partially solvated model alpha-helices, one corresponding to a more exposed and the other to a more buried structure, are compared to the fully solvated and unsolvated (gas phase) simulations. The dependence of the amide I spectra on the orientation of the partially solvated helix with respect to the solvent and effects of solvation on the amide I' of 13C isotopically substituted alpha-helices are also investigated. The partial exposure to solvent causes significant broadening of the amide I' bands due to differences in the vibrational frequencies of the explicitly solvated and unsolvated amide groups. The different degree of partial solvation is reflected primarily in the frequency shifts of the unsolvated (buried) amide group vibrations. Depending on which side of the alpha-helix is exposed to solvent, the simulated IR band-shapes exhibit significant changes, from broad and relatively featureless to distinctly split into two maxima. The simulated amide I' VCD band-shapes for the partially solvated alpha-helices parallel the broadening of the IR and exhibit more sign variation, but generally preserve the sign pattern characteristic of the alpha-helical structures and are much less dependent on the alpha-helix orientation with respect to the solvent. The simulated amide I' IR spectra for the model peptides with explicitly hydrogen-bonded water are consistent with the experimental data for small alpha-helical proteins at very low temperatures, but overestimate the effects of solvent on the protein spectra at ambient temperatures, where the peptide-water hydrogen bonds are weakened by thermal motion.     

Correlation between pulse radiolysis and positron annihilation techniques data

The inhibition and enhancement constants for positronium (Ps) formation in water for 50 solutes are reported; they are shown to be strongly correlated to the rate constants for hydrated electron, k_eaq⁻ or for OH scavenging, k_OH, measured in pulse radiolysis experiments, respectively. While most of the solutes appear able to inhibit completely Ps formation at high enough concentration, some lead to limited inhibition only, and the fraction ƒ of Ps thus suppressed is characteristic of the solvent. These data lend support to the spur model of Ps formation and suggest that the fully solvated particles are not likely to be involved in this process. On this basis, a provisional model for Ps formation is proposed and discussed.     

Calculation of wave‐functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. II. Application of the local basis equation

The application of the local basis equation (Ferenczy and Adams, J. Chem. Phys. 2009 , 130, 134108) in mixed quantum mechanics/molecular mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) methods is investigated. This equation is suitable to derive local basis nonorthogonal orbitals that minimize the energy of the system and it exhibits good convergence properties in a self‐consistent field solution. These features make the equation appropriate to be used in mixed QM/MM and QM/QM methods to optimize orbitals in the field of frozen localized orbitals connecting the subsystems. Calculations performed for several properties in divers systems show that the method is robust with various choices of the frozen orbitals and frontier atom properties. With appropriate basis set assignment, it gives results equivalent with those of a related approach [G. G. Ferenczy previous paper in this issue] using the Huzinaga equation. Thus, the local basis equation can be used in mixed QM/MM methods with small size quantum subsystems to calculate properties in good agreement with reference Hartree–Fock–Roothaan results. It is shown that bond charges are not necessary when the local basis equation is applied, although they are required for the self‐consistent field solution of the Huzinaga equation based method. Conversely, the deformation of the wave‐function near to the boundary is observed without bond charges and this has a significant effect on deprotonation energies but a less pronounced effect when the total charge of the system is conserved. The local basis equation can also be used to define a two layer quantum system with nonorthogonal localized orbitals surrounding the central delocalized quantum subsystem. © 2013 Wiley Periodicals, Inc.     

Nanotube confinement denatures protein helices

In striking contrast to simple polymer physics theory, which does not account for solvent effects, we find that physical confinement of solvated biopolymers decreases solvent entropy, which in turn leads to a reduction in the organized structural content of the polymer. Since our theory is based on a fundamental property of water-protein statistical mechanics, we expect it to have broad implications in many biological and material science contexts.     

The incorporation of hydration forces determined by continuum electrostatics into molecular mechanics simulations

A new technique is presented for incorporating hydration forces into molecular mechanics simulations. The method assumes the classical continuum approximation, where a solvated molecule is represented as a low-dielectric cavity of arbitrary shape embedded in a continuous region of high dielectric constant. Electrostatic effects are computed by first calculating the distribution of polarization charge (induced by the configuration of solute fixed charges) at the molecular surface. The hydration force at a particular atom is then found as the sum of the coulombic interaction with the induced surface charge, plus a purely mechanical contribution that arises from the pressure of the polarized solvent as it is pulled toward the solute. A procedure is developed to use the computed hydration forces in conjunction with the CHARMM molecular mechanics package to carry out energy minimizations in which the effects of solvation are explicitly included. This new technique also allows a detailed analysis of the relative balance of coulombic, hydration, and steric energies as a function of molecular conformation. The method is applied to the test case of a zwitterionic tripeptide (LYS-GLY-GLU), and the computational results suggest that hydration effects can play a significant role in determining a stable conformation for a solvated polar molecule. The future application to larger molecules is discussed.     

Empirical solvent correction for multiple amide group vibrational modes

Previously proposed solvent correction to the amide I peptide vibration was extended so that it can be applied to a general solvated chromophore. The combined molecular and quantum mechanics (MMQM) method is based on a linear dependence of harmonic force field and intensity tensor components of the solute on solvent electrostatic field. For N-methylacetamide, realistic solvent frequency and intensity changes as well as inhomogeneous band widths were obtained for amide A, I, II , and III modes. A rather anomalous basis set size dependence was observed for the amide A and I vibrations, when bigger basis lead to narrowing of spectral bands and lesser molecular sensibility to the environment. For a model alpha-helical peptide, a W-shape of the vibrational circular dichroism signal observed in deuterated solvent for the amide I band was reproduced correctly, unlike with previous vacuum models.     

7Li PGSE diffusion measurements on LiPPh2: a solvent dependence of the structure

The first application of 7Li pulsed-gradient spin-echo (PGSE) diffusion methods to structural lithium chemistry is reported. The data, which provide quantitative diffusion constants at 155 K, lead to a new method of estimating solvent viscosity at this temperature and clearly show a solvent dependence for the structure of LiPPh2. In THF, LiPPh2 exists as a mononuclear solvated species, whereas in Et2O, a dinuclear structure is found. D values for the model compound PHPh2 in THF have been measured.     

Benchmarking the multipole shielding polarizability/reaction field approach to solvation against QM/MM: applications to the shielding constants of N-methylacetamide

We present a benchmark study of a combined multipole shielding polarizability/reaction field (MSP/RF) approach to the calculation of both specific and bulk solvation effects on nuclear magnetic shielding constants of solvated molecules. The MSP/RF scheme is defined by an expansion of the shielding constants of the solvated molecule in terms of electric field and field gradient property derivatives derived from single molecule ab initio calculations. The solvent electric field and electric field gradient are calculated based on data derived from molecular dynamics simulations, thereby accounting for solute-solvent dynamical effects. The MSP/RF method is benchmarked against polarizable quantum mechanics/molecular mechanics (QM/MM) calculations. The best agreement between the MSP/RF and QM/MM approaches is found by truncating the electric field expansion in the MSP/RF approach at the linear electric field level which is due to the cancelation of errors. In addition, we investigate the sensitivity of the results due to the choice of one-electron basis set in the ab initio calculations of the property derivatives and find that these derivatives are affected by the basis set in a way similar to the shielding constants themselves.     

The implementation of a fast and accurate QM/MM potential method in Amber

Version 9 of the Amber simulation programs includes a new semi-empirical hybrid QM/MM functionality. This includes support for implicit solvent (generalized Born) and for periodic explicit solvent simulations using a newly developed QM/MM implementation of the particle mesh Ewald (PME) method. The code provides sufficiently accurate gradients to run constant energy QM/MM MD simulations for many nanoseconds. The link atom approach used for treating the QM/MM boundary shows improved performance, and the user interface has been rewritten to bring the format into line with classical MD simulations. Support is provided for the PM3, PDDG/PM3, PM3CARB1, AM1, MNDO, and PDDG/MNDO semi-empirical Hamiltonians as well as the self-consistent charge density functional tight binding (SCC-DFTB) method. Performance has been improved to the point where using QM/MM, for a QM system of 71 atoms within an explicitly solvated protein using periodic boundaries and PME requires less than twice the cpu time of the corresponding classical simulation.     

Further studies of the spur process of positronium formation in mixtures of organic liquids

To test some predictions of the spur model of positronium (Ps) formation, positron lifetime studies were made of the following binary organic mixtures: (a) carbondisulphide mixtures with n-tetradecane, n-hexane, isooctane, neopentane, and tetramethylsilane (TMS); (b) neopentane mixtures with methanol, ethanol, cyclohexanol, and methylcyclohexane; (c) cis-2-butene/trans-2-butene, and benzene/ethanol. The results were in agreement with the model. A minimum in the Ps yield versus CS₂ concentration, explained as being caused by electron localization on CS₂ at low and delocalization on several CS₂ molecules at higher CS₂ concentration, depended on the electron work function V_o of the solvent. This minimum was pronounced (shallow or absent) at high (low) V_o. Solvation of electrons and positrons in alcohol clusters strongly influenced the Ps yield for the neopentane mixtures. The Ps yield was higher in cis- than in trans-2-butene. The Ps formation process in polar liquids is discussed. Experiment facts do not preclude that Ps is also formed by the encounter pair process of fully solvated particles in the positron spur.     

Solvent effects on glycine. I. A supermolecule modeling of tautomerization via intramolecular proton transfer

The relative stabilities of glycine tautomers involved in the intramolecular proton transfer are investigated computationally by considering glycine-water complexes containing up to five water molecules. The supermolecule results are compared with continuum calculations. Specific solute-solvent interactions and solvent induced changes in the solute wave function are considered using the natural bond orbitals (NBO) method. The stabilization of the zwitterion upon solvation is explained by the changes in the wave functions localized on the forming and breaking bonds as well as by the different interaction energies in the zwitterionic and neutral clusters. Only the neutral species exist in mono- and dihydrated clusters and in the gas phase. In the smaller clusters, zwitterions are mainly stabilized by conformational effects, whereas in larger clusters, in particular when glycine is solvated on both sides of its heavy atom backbone, polarization effects dominate the stability of a given tautomer. Generally, the strength of the solute-solvent interactions is governed by the intermolecular charge transfer interactions. As the solvation progresses, the hypothetical gaseous zwitterion is better solvated than the gaseous neutral, making zwitterion to neutral tautomerization progressively less exothermic for clusters containing up to three water molecules, and endothermic for larger clusters. The neutral isomer does not exist for some solvent arrangements with five water molecules. Only solvent arrangements in which water molecules do not interact with the reactive proton are considered. Hence, the experimentally observed double well potential energy surface may be due to such an interaction or to a different reaction mechanism.     

Solvation effect in thermal decomposition of 2,2′-azoisobutyronitrile

The solvation effect in the thermal decomposition of a radical initiator (AIBN) in monomer–solvent mixtures is discussed. Equations were derived which comprise the initiator decomposition constant as a function of the monomer mole fraction for chosen types of solvation. In addition, equations were deduced presenting the concentrations and partial relative decomposition rates for the solvated initiator species as a function of the monomer mole fraction. The equations obtained were compared to the experimental literature data and possible dependences of decomposition constants on monomer concentration were simulated for various solvated species. The simulated relationships were found to be straight lines, curves of saturated type (possessing a plateau), S-shaped curves, and maximum or minimum curves. © 1995 John Wiley & Sons, Inc.     

TRIPLET, RADICAL ANION AND RADICAL CATION SPECTRA OF FUROCOUMARINS

Abstract— Absorption spectra of triplets, radical anions and radical cations of four furocoumarins, psoralen (Ps), 8-methoxypsoralen (8MOP), 5-methoxypsoralen (5MOP) and 3-carbethoxypsoralen (3CPs), have been determined by laser flash photolysis and pulse radiolysis. The triplet spectra of 8MOP, 5MOP and 3CPs are strongly modified when going from an H-bonding solvent such as water to a non H-bonding solvent as benzene or acetonitrile while the triplet spectrum of Ps is solvent independent. Theoretical considerations using a CNDO/S method are able to explain the existence of these two different triplets. For 8MOP, 5MOP and 3CPs in water the triplets might be considered as triplet exciplexes ³(FC^δ-. H₂O^δ+) consistent with these triplet spectra being similar to the spectra of the corresponding radical anions.     

Wave model for conservative bound systems

In the hidden variable theory, Bohm proved a connection between the Schrodinger and Hamilton-Jacobi equations and showed the existence of classical paths, for which the generalized Bohr quantization condition is valid. In this paper we prove similar properties, starting from the equivalence between the Schrodinger and wave equations in the case of the conservative bound systems. Our approach is based on the equations and postulates of quantum mechanics without using any additional postulate. Like in the hidden variable theory, the above properties are proven without using the approximation of geometrical optics or the semiclassical approximation. Since the classical paths have only a mathematical significance in our analysis, our approach is consistent with the postulates of quantum mechanics.