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The molecular origin of the energy produced by the ATP hydrolysis has been one of the long-standing fundamental issues. A classical view is that the negative hydrolysis free energy of ATP originates from intramolecular effects connected with the backbone P-O bond, so called "high-energy bond". On the other hand, it has also been recognized that solvation effects are essential in determining the hydrolysis free energy. Here, using the 3D-RISM-SCF (three-dimensional reference interaction site model self-consistent field) theory that integrates the ab initio quantum chemistry method and the statistical mechanical theory of liquids, we investigate the molecular origin of hydrolysis free energy of pyrophosphate, an ATP analogue, in water. We demonstrate that our theory quantitatively reproduces the experimental results without the use of empirical parameters. We clarify the crucial role of water in converting the hydrolysis free energy in the gas phase determined solely by intramolecular effects, which ranges from endothermic, thermoneutral, to highly exothermic depending on the charged state of pyrophosphate, into moderately exothermic in the aqueous phase irrespective of the charged state as observed in experimental data. We elucidate that this is brought about by different natures of solute-water interactions depending on the charged state of solute species: the hydration free energy of low-charged state is mainly subjected to short-range hydrogen-bonds, while that of high-charged state is dominated by long-range electrostatic interactions. We thus provide unambiguous evidence on the critical role of water in determining the ATP hydrolysis free energy.

Amide I local mode frequencies and vibrational coupling constants in various multiple-stranded antiparallel β-sheet polyalanines are calculated by using the semiempirical calculation method and Hessian matrix reconstruction methods. The amide I local mode frequency is strongly dependent on the nature and number of hydrogen bonds. Vibrational couplings among amide I local modes in the multiple-stranded β-sheets are shown to be fully characterized by eight different coupling constants. The intrastrand coupling constants are found to be much smaller than the interstrand ones. Introducing newly defined inverse participation ratios and phase-correlation factors, the extent of two-dimensional delocalization and the vibrational phase relationship of amide I normal modes are elucidated. The A−E1 frequency splitting magnitude is shown to be strongly dependent on the number of strands but not on the length of each strand. A reduced one-dimensional Frenkel exciton model is used to describe the observed A−E1 frequenc...

Chain length and site dependencies of amide I local mode frequencies of α-helical polyalanines are theoretically studied by carrying out semiempirical quantum chemistry calculations. A theoretical model that can be used to quantitatively predict both the local amide I mode frequencies and coupling constants between two different local amide I modes is developed. Using this theoretical model and performing molecular dynamics simulation of an α-helical polyalanine in liquid water, we investigate conformational fluctuation and hydrogen-bonding dynamics by monitoring amide I frequency fluctuations. The instantaneous normal-mode analysis method is used to obtain densities of states of the one- and two-exciton bands and to quantitatively investigate the extent of delocalization of the instantaneous amide I normal modes. Also, by introducing a novel concept of the so-called weighted phase-correlation factor, the symmetric natures of the delocalized amide I normal modes are elucidated, and it is also shown that t...

Synthesis of a novel pyrene derivative sensor (1) and its intermolecular binding pattern to Cu(2+) in CH(3)CN were investigated. Upon Cu(2+) binding, the sensor exhibited a strong static excimer emission at 460 nm, along with a weak monomer emission at 388 nm. The excimer emission intensity induced by the Cu(2+) ion declined as the spacer length between the pyrene and quinolinylamide unit increased. The Cu(2+) ion-induced self-assembled pyrenyl excimer formation is rationalized by fluorescence experiments and theoretical DFT calculations.

Linear and nonlinear IR spectroscopic studies of nucleic acids can provide crucial information on solution conformations of DNA double helix and its complex with other molecules. Carrying out density functional theory calculations of A-, B-, and Z-form DNA's, the authors obtained vibrational spectroscopic properties as well as coupling constants between different basis modes. The vibrational couplings that determine the extent of exciton delocalization are strongly dependent on DNA conformation mainly because the interlayer distance between two neighboring base pairs changes with respect to the DNA conformation. The Z-DNA has comparatively small interlayer vibrational coupling constants so that its vibrational spectrum depends little on the number of base pairs, whereas the A-DNA shows a notable dependency on the size. Furthermore, it is shown that a few distinctively different line shape changes in both IR and two-dimensional IR spectra as the DNA conformation changes from B to A or from B to Z can be used as marker bands and characteristic features distinguishing different DNA conformations.

Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene∕CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol’s first solvent shell.

In Paper I, we studied vibrational properties of normal bases, base derivatives, Watson-Crick base pairs, and multiple layer base pair stacks in the frequency range of 1400-1800 cm(-1). However, typical IR absorption spectra of single- and double-stranded DNA have been measured in D(2)O solution. Consequently, the more relevant bases and base pairs are those with deuterium atoms in replacement with labile amino hydrogen atoms. Thus, we have carried out density functional theory vibrational analyses of properly deuterated bases, base pairs, and stacked base pair systems. In the frequency range of interest, both aromatic ring deformation modes and carbonyl stretching modes appear to be strongly IR active. Basis mode frequencies and vibrational coupling constants are newly determined and used to numerically simulate IR absorption spectra. It turns out that the hydration effects on vibrational spectra are important. The numerically simulated vibrational spectra are directly compared with experiments. Also, the (18)O-isotope exchange effect on the poly(dG):poly(dC) spectrum is quantitatively described. The present calculation results will be used to further simulate two-dimensional IR photon echo spectra of DNA oligomers in the companion Paper III.

Hydration effects on the C[Triple Bond]N stretching mode frequencies of MeCN and MeSCN are investigated by carrying out ab initio calculations for a number of MeCN-water and MeSCN-water complexes with varying number of water molecules. It is found that the CN frequency shift induced by the hydrogen-bonding interactions with water molecules originate from two different ways to form hydrogen bonds with the nitrogen atom of the CN group. Considering the MeCN- and MeSCN-water cluster calculation results as databases, we first examined the validity of vibrational Stark effect relationship between the CN frequency and the electric field component parallel to the CN bond and found no strong correlation between the two. However, taking into account of additional electric field vector components is a simple way to generalize the vibrational Stark theory for the nitrile chromophore. Also, the electrostatic potential calculation method has been proposed and examined in detail. It turned out that the interactions of water molecules with nitrogen atom's lone pair orbital and with nitrile pi orbitals can be well described by the electrostatic potential calculation method. The present computational results will be of use to quantitatively simulate various linear and nonlinear vibrational spectra of nitrile compounds in solutions.

A theoretical description of the vibrational excitons in DNA is presented by using the vibrational basis mode theory developed in Papers I and II. The parameters obtained from the density functional theory calculations, such as vibrational coupling constants and basis mode frequencies, are used to numerically simulate two-dimensional (2D) IR spectra of dG(n):dC(n) and dA(n):dT(n) double helices with n varying from 1 to 10. From the molecular dynamics simulations of dG(5)C(5) and dA(5)T(5) double helices in D(2)O solution, it is found that the thermally driven internal motions of these systems in an aqueous solution do not induce strong fluctuations of basis mode frequencies nor vibrational couplings. In order to construct the two-exciton Hamiltonian, the vibrational anharmonicities of eight basis modes are obtained by carrying out B3LYP6-31G(*) calculations for the nine basis modes. The simulated 2D IR spectra of dG(n):dC(n) double helix in D(2)O solution are directly compared with closely related experimental results. The 2D IR spectra of dG(n):dC(n) and dA(n):dT(n) are found to be weakly dependent on the number of base pairs. The present work demonstrates that the computational procedure combining quantum chemistry calculation and molecular dynamics simulation methods can be of use to predict 2D IR spectra of nucleic acids in solutions.

Carrying out density functional theory calculations of four DNA bases, base derivatives, Watson-Crick (WC) base pairs, and multiple-layer base pair stacks, we studied vibrational dynamics of delocalized modes with frequency ranging from 1400 to 1800 cm(-1). These modes have been found to be highly sensitive to structure fluctuation and base pair conformation of DNA. By identifying eight fundamental basis modes, it is shown that the normal modes of base pairs and multilayer base pair stacks can be described by linear combinations of these vibrational basis modes. By using the Hessian matrix reconstruction method, vibrational coupling constants between the basis modes are determined for WC base pairs and multilayer systems and are found to be most strongly affected by the hydrogen bonding interaction between bases. It is also found that the propeller twist and buckle motions do not strongly affect vibrational couplings and basis mode frequencies. Numerically simulated IR spectra of guanine-cytosine and adenine-thymine bases pairs as well as of multilayer base pair stacks are presented and described in terms of coupled basis modes. It turns out that, due to the small interlayer base-base vibrational interactions, the IR absorption spectrum of multilayer base pair system does not strongly depend on the number of base pairs.

The antiparallel and parallel beta sheets are two of the most abundant secondary structures found in proteins. Although various spectroscopic methods have been used to distinguish these two different structures, the linear spectroscopic measurements could not provide incisive information for distinguishing an antiparallel beta sheet from a parallel beta sheet. After carrying out quantum-chemistry calculations and model simulations, we show that the polarization-controlled two-dimensional (2D) IR photon echo spectroscopy can be of critical use in distinguishing these two different beta sheets. Particularly, the ratio between the diagonal peak and the cross peak is found to be strongly dependent on the quasi-2D array of the amide I local-mode transition dipole vectors. The relative intensities of the cross peaks in the 2D difference spectrum of an antiparallel beta sheet are significantly larger than those of the diagonal peaks, whereas the cross-peak amplitudes in the 2D difference spectrum of a parallel beta sheet are much weaker than the main diagonal-peak amplitudes. A detailed discussion on the origin of the diagonal- and cross-peak intensity distributions of both the antiparallel and parallel beta sheets is presented by examining vibrational exciton delocalization, relative angles between two different normal-mode transition dipoles, and natures of the cross peaks in the 2D difference spectrum.