Influence of high pressure on optical impurity spectra

Expressions are derived for inhomogeneous band shapes of impurity spectra in highly compressed glassy matrices. Intermolecular guest-host interactions are approximated to isotropic two-body Lennard-Jones 6-12 potentials having different parameters in the ground state and the excited state. Calculated shifts and widths are compared to published values for the absorption spectra of phenanthrene, anthracene [B. Y. Okamoto and H. G. Drickamer, J. Chem. Phys. 61, 2870 (1974)], and several polymethine dyes [G. A. Samara et al., J. Chem. Phys. 37, 1482 (1962)] embedded in polymer hosts and subject to pressures up to 140 kbars. The magnitudes of barochromic shifts of the band maxima and the inhomogeneous broadening suggest that the equilibrium coordinates of the excited state are typically less by 5+/-2%.     

Bond alternation, polarizability, and resonance detuning in methine dyes

We derive structure-property relationships for methine ("Brooker") dyes relating the color of the dye and its symmetric parents to its bond alternation in the ground state and also to the dipole properties associated with its low-lying charge-resonance (or charge-transfer) transition. We calibrate and test these relationships on an array of different protonation states of the green fluorescent protein chromophore motif (an asymmetric halochromic methine dye) and its symmetric parent dyes. The relationships rely on the assumption that the diabatic states that define the Platt model for methine dye color [J. R. Platt, J. Chem. Phys. 25, 80 (1956)] can also be distinguished by their single-double bond alternation and by their charge localization character. These assumptions are independent of the primary constraint that defines the diabatic states in the Platt model--specifically, the Brooker deviation rule for methine dyes [L. G. S. Brooker, Rev. Mod. Phys. 14, 275 (1942)]. Taking these assumptions, we show that the Platt model offers an alternate route to known structure-property relationships between the bond length alternation and the quadratic nonlinear polarizability β. We show also that the Platt model can be parameterized without the need for synthesis of the symmetric parents of a given dye, using the dipole data obtained through spectroscopic measurements. This suggests that the Platt model parameters may be used as independent variables in free-energy relationships for chromophores whose symmetric parents cannot be synthesized or chromophores strongly bound to biomolecular environments. The latter category includes several recently characterized biomolecular probe constructs. We illustrate these concepts by an analysis of previously reported electroabsorption and second-harmonic generation experiments on green fluorescent proteins.     

Time-dependent wave packet study on trans-cis isomerization of HONO driven by an external field

The present paper is devoted to a full quantum mechanical study of the cis-->trans isomerization of HONO. In contrast to our previous study [Richter et al., J. Chem. Phys. 120, 6072 (2004)], the dynamics is now performed in the presence of an external time-dependent field in order to be closer to experimental conditions. A six-dimensional dipole surface is computed. Using a previously developed potential energy surface [Richter et al., J. Chem. Phys. 120, 1306 (2004)], all eigenstates up to 4000 cm(-1) are calculated. We simulate the dynamics during and after excitation by an electromagnetic pulse whose parameters are chosen to efficiently trigger the isomerization. Our investigations show that there is a selective isomerization pathway.     

The use of atomic intrinsic polarizabilities in the evaluation of the dispersion energy

The recent approach presented by Becke and Johnson [J. Chem. Phys. 122, 154104 (2005); 123, 024101 (2005); 123, 154101 (2005); 124, 174104 (2006); 124, 014104 (2006)] for the evaluation of dispersion interactions based on the properties of the exchange-hole dipole moment is combined with a Hirshfeld-type partitioning for the molecular polarizabilities into atomic contributions, recently presented by some of the present authors [A. Krishtal et al., J. Chem. Phys. 125, 034312 (2006)]. The results on a series of nine dimers, involving neon, methane, ethene, acetylene, benzene, and CO(2), taken at their equilibrium geometry, indicate that when the C(6), C(8), and C(10) terms are taken into account, the resulting dispersion energies can be obtained deviating 3% or 8% from high level literature data [E. R. Johnson and A. D. Becke, J. Chem. Phys. 124, 174104 (2006)], without the use of a damping function, the only outlier being the parallel face-to-face benzene dimer.     

Electrostatics of proteins in dielectric solvent continua. II. First applications in molecular dynamics simulations

In the preceding paper by Stork and Tavan, [J. Chem. Phys. 126, 165105 (2007)], the authors have reformulated an electrostatic theory which treats proteins surrounded by dielectric solvent continua and approximately solves the associated Poisson equation [B. Egwolf and P. Tavan, J. Chem. Phys. 118, 2039 (2003)]. The resulting solution comprises analytical expressions for the electrostatic reaction field (RF) and potential, which are generated within the protein by the polarization of the surrounding continuum. Here the field and potential are represented in terms of Gaussian RF dipole densities localized at the protein atoms. Quite like in a polarizable force field, also the RF dipole at a given protein atom is induced by the partial charges and RF dipoles at the other atoms. Based on the reformulated theory, the authors have suggested expressions for the RF forces, which obey Newton's third law. Previous continuum approaches, which were also built on solutions of the Poisson equation, used to violate the reactio principle required by this law, and thus were inapplicable to molecular dynamics (MD) simulations. In this paper, the authors suggest a set of techniques by which one can surmount the few remaining hurdles still hampering the application of the theory to MD simulations of soluble proteins and peptides. These techniques comprise the treatment of the RF dipoles within an extended Lagrangian approach and the optimization of the atomic RF polarizabilities. Using the well-studied conformational dynamics of alanine dipeptide as the simplest example, the authors demonstrate the remarkable accuracy and efficiency of the resulting RF-MD approach.     

Local response dispersion method. II. Generalized multicenter interactions

Recently introduced local response dispersion method [T. Sato and H. Nakai, J. Chem. Phys. 131, 224104 (2009)], which is a first-principles alternative to empirical dispersion corrections in density functional theory, is implemented with generalized multicenter interactions involving both atomic and atomic pair polarizabilities. The generalization improves the asymptote of intermolecular interactions, reducing the mean absolute percentage error from about 30% to 6% in the molecular C(6) coefficients of more than 1000 dimers, compared to experimental values. The method is also applied to calculations of potential energy curves of molecules in the S22 database [P. Jure?ka et al., Phys. Chem. Chem. Phys. 8, 1985 (2006)]. The calculated potential energy curves are in a good agreement with reliable benchmarks recently published by Molnar et al. [J. Chem. Phys. 131, 065102 (2009)]. These improvements are achieved at the price of increasing complexity in the implementation, but without losing the computational efficiency of the previous two-center (atom-atom) formulation. A set of different truncations of two-center and three- or four-center interactions is shown to be optimal in the cost-performance balance.     

Electronic spectroscopy of molecules in superfluid helium nanodroplets: an excellent sensor for intramolecular charge redistribution

Electronic spectra of molecules doped into superfluid (4)He nanodroplets reveal important details of the microsolvation in superfluid helium. The vibrational fine structure in the electronic spectra of phthalocyanine derivatives and pyrromethene dye molecules doped into superfluid helium droplets have been investigated. Together with previous studies on anthracene derivatives [J. Chem. Phys.2010, 133, 114505] and 3-hydroxyflavone [J. Chem. Phys.2009, 131, 194307], the line shapes vary between two limiting cases, namely, sharp Lorentzians and nonresolved vibrational fine structure. All different spectral signatures are initiated by the same effect, namely, the change of the electron density distribution initiated by the electronic excitation. This change can be quantified by the difference of the electrostatic moments of the molecule in the electronic ground state and the corresponding Franck-Condon point in the excited state. According to the experimental data, electronic spectroscopy suffers from drastic line broadening when accompanied by significant changes of the charge distribution, in particular, changes of the dipole moment. Vice versa, the vibrational fine structure in electronic spectra of molecules doped into helium droplets is highly sensitive to changes of the electron density distribution.     

Polarizable and flexible model for ethanol

A polarizable, flexible model for ethanol is obtained based on an extensive series of B3LYP/6-311++G(d,p) calculations and molecular dynamics simulations. The ethanol model includes electric-field dependence in both the atomic charges and the intramolecular degrees of freedom. Field-dependent intramolecular potentials have been attempted only once previously, for OH and HH stretches in water [P. Cicu et al., J. Chem. Phys. 112, 8267 (2000)]. The torsional potential involving the hydrogen-bonding hydrogen in ethanol is found to be particularly field sensitive. The methodology for developing field-dependent potentials can be readily generalized to other molecules and is discussed in detail. Molecular dynamics simulations of bulk ethanol are performed and the results are assessed based on comparisons with the self-diffusion coefficient [N. Karger et al., J. Chem. Phys. 93, 3437 (1990)], dielectric constant [J. T. Kindt and C. A. Schmuttenmaer, J. Phys. Chem. 100, 10373 (1996)], enthalpy of vaporization [R. C. Wilhoit and B. J. Zwolinski, J. Phys. Chem. Ref. Data, Suppl. 2, 2 (1973)], and experimental interatomic distributions [C. J. Benmore and Y. L. Loh, J. Chem. Phys. 112, 5877 (2000)]. The simultaneous variation of the atomic charges and the intramolecular potentials requires modified equations of motion and a multiple time step algorithm has been implemented to solve these equations. The article concludes with a discussion of the bulk structure and properties with an emphasis on the hydrogen bonding network.     

Linear scaling computation of the Fock matrix. VII. Periodic density functional theory at the Gamma point

Linear scaling quantum chemical methods for density functional theory are extended to the condensed phase at the Gamma point. For the two-electron Coulomb matrix, this is achieved with a tree-code algorithm for fast Coulomb summation [M. Challacombe and E. Schwegler, J. Chem. Phys. 106, 5526 (1997)], together with multipole representation of the crystal field [M. Challacombe, C. White, and M. Head-Gordon, J. Chem. Phys. 107, 10131 (1997)]. A periodic version of the hierarchical cubature algorithm [M. Challacombe, J. Chem. Phys. 113, 10037 (2000)], which builds a telescoping adaptive grid for numerical integration of the exchange-correlation matrix, is shown to be efficient when the problem is posed as integration over the unit cell. Commonalities between the Coulomb and exchange-correlation algorithms are discussed, with an emphasis on achieving linear scaling through the use of modern data structures. With these developments, convergence of the Gamma-point supercell approximation to the k-space integration limit is demonstrated for MgO and NaCl. Linear scaling construction of the Fockian and control of error is demonstrated for RBLYP6-21G* diamond up to 512 atoms.     

Effect of polymer microenvironment on excitation energy migration and transfer

Excitation energy transfer between the dye pair acriflavine (donor) to rhodamine-6G (acceptor) in various polymers [polyvinyl alcohol (PVA), cellulose acetate, and polymethyl methacrylate (PMMA)] was studied using steady-state and time-resolved fluorescence spectroscopy at room temperature. In all these polymers, at higher acceptor concentrations, direct energy transfer from acriflavine to rhodamine-6G followed the F?rster theory, which is indicated by the agreement in the values of the observed critical transfer distance with that calculated from spectral overlap. On the other hand, at low acceptor concentrations, the excitation energy migration influences the kinetics, resulting in a significantly higher value of the observed critical transfer distance, which is explained on the basis of Loring et al. (Loring, R. F.; Anderson, H. C.; Fayer, M. D. J. Chem. Phys. 1984, 80, 5731-5744) and Huber (Huber, D. L. Phys. Rev. B: Condens. Matter Mater. Phys. 1979, 20 2307-2314) theories. It was observed that the spectral overlap for donor-donor transport (excitation migration) and donor-acceptor transfer (energy transfer) and thereby other energy transfer parameters were influenced by the microenvironment of the polymers. The efficiency of energy transfer (eta) was the highest in PMMA and the lowest in PVA. Further, the study of acceptor dynamics under energy transfer showed that the rise time of the acceptor also depends on the nature of the polymer microenvironment.     

Statistical mechanical theory for steady state systems. VI. Variational principles

Several variational principles that have been proposed for nonequilibrium systems are analyzed. These include the principle of minimum rate of entropy production due to Prigogine [Introduction to Thermodynamics of Irreversible Processes (Interscience, New York, 1967)], the principle of maximum rate of entropy production, which is common on the internet and in the natural sciences, two principles of minimum dissipation due to Onsager [Phys. Rev. 37, 405 (1931)] and to Onsager and Machlup [Phys. Rev. 91, 1505 (1953)], and the principle of maximum second entropy due to Attard [J. Chem.. Phys. 122, 154101 (2005); Phys. Chem. Chem. Phys. 8, 3585 (2006)]. The approaches of Onsager and Attard are argued to be the only viable theories. These two are related, although their physical interpretation and mathematical approximations differ. A numerical comparison with computer simulation results indicates that Attard's expression is the only accurate theory. The implications for the Langevin and other stochastic differential equations are discussed.     

Accurate atomic Gaussian basis functions for second-row atoms: Small split-valence 3-21SP and 4-22SP basis sets

Small split-valence Gaussian 3-21SP and 4-22SP basis sets, previously reported for the first-row atoms [Chem. Phys. Lett., 229 , 151 (1996)], have been extended for the second-row elements of the Periodic Table. The total energies of the ground states of the second-row atoms calculated with the new basis sets are significantly lower than those obtained with the well-known 3-21G (J. Am. Chem. Soc., 104 , 2797 (1982)] and 4-31G [J. Chem. Phys., 56 , 5255 (1972)] basis sets. This is because, as first noted in our previous work for first-row atoms, that the 3-21G and 4-31G basis sets only correspond to a local minimum of the Hartree–Fock energy functional, which is relatively far from its global minimum. The proposed basis sets have been tested by performing geometry optimizations and calculations of normal frequencies in the harmonic approximation of some diatomic and polyatomic molecules at the Hartree–Fock level. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1200–1210     

Predicting the infrared transition intensities in the Ar-HF complex: the key role of the dipole moment surface accuracy

The method proposed earlier for the generation of the full-dimensional energy surface for van der Waals complexes [P. Jankowski, J. Chem. Phys. 121, 1655 (2004)] is used to obtain a fulldimensional dipole moment surface for the atom-diatom complex in calculations based on the coupled-cluster with single, double, and noniterative triple excitation approach and the aug-cc-pVQZ basis sets. This surface has been employed to calculate transition intensities of the infrared spectra of Ar-HF. Special attention has been paid to study the problem of relative intensities of the different bands which have not been properly predicted within the long-range models of the dipole moment [A. E. Thornley and J. M. Hutson, J. Chem. Phys. 101, 5578 (1994)]. The intensities calculated with the present dipole moment surface agree very well with the experimental data, which indicate that the short-range interactions significantly affect the dipole moment surface and the calculated intensities. To investigate the role of the accuracy of the dipole moment surface on infrared transition intensities in atom-diatom complexes, four models of increasing complexity are studied. Their performance is shown to strongly depend on the region of the interaction energy surface probed by the initial and final states of the individual transitions.     

Assessment of the efficiency of long-range corrected functionals for some properties of large compounds

Using the long-range correction (LC) density functional theory (DFT) scheme introduced by Iikura et al. [J. Chem. Phys. 115, 3540 (2001)] and the Coulomb-attenuating model (CAM-B3LYP) of Yanai et al. [Chem. Phys. Lett. 393, 51 (2004)], we have calculated a series of properties that are known to be poorly reproduced by standard functionals: Bond length alternation of pi-conjugated polymers, polarizabilities of delocalized chains, and electronic spectra of extended dyes. For each of these properties, we present cases in which traditional hybrid functionals do provide accurate results and cases in which they fail to reproduce the correct trends. The quality of the results is assessed with regard to experimental values and/or data arising from electron-correlated wave function approaches. It turns out that (i) both LC-DFT and CAM-B3LYP provide an accurate bond length alternation for polyacetylene and polymethineimine, although for the latter they decrease slightly too rapidly with chain length. (ii) The LC generalized gradient approximation and MP2 polarizabilities of long polyphosphazene and polymethineimine oligomers agree almost perfectly. In the same way, CAM-B3LYP corrects the major part of the B3LYP faults. (iii) LC and CAM techniques do not help in correcting the nonrealistic evolution with chain length of the absorption wavelengths of cyanine derivatives. In addition, though both schemes significantly overestimate the ground to excited state transition energy of substituted anthraquinone dyes, they provide a more consistent picture once a statistical treatment is performed than do traditional hybrid functionals.     

A post-Hartree-Fock model of intermolecular interactions: inclusion of higher-order corrections

We have previously demonstrated that the dipole moment of the exchange hole can be used to derive intermolecular C(6) dispersion coefficients [J. Chem. Phys. 122, 154104 (2005)]. This was subsequently the basis for a novel post-Hartree-Fock model of intermolecular interactions [J. Chem. Phys. 123, 024101 (2005)]. In the present work, the model is extended to include higher-order dispersion coefficients C(8) and C(10). The extended model performs very well for prediction of intermonomer separations and binding energies of 45 van der Waals complexes. In particular, it performs twice as well as basis-set extrapolated MP2 theory for dispersion-bound complexes, with minimal computational cost.     

Water models based on a single potential energy surface and different molecular degrees of freedom

Up to now it has not been possible to neatly assess whether a deficient performance of a model is due to poor parametrization of the force field or the lack of inclusion of enough molecular properties. This work compares several molecular models in the framework of the same force field, which was designed to include many-body nonadditive effects: (a) a polarizable and flexible molecule with constraints that account for the quantal nature of the vibration [B. Hess, H. Saint-Martin, and H. J. C. Berendsen, J. Chem. Phys. 116, 9602 (2002), H. Saint-Martin, B. Hess, and H. J. C. Berendsen, J. Chem. Phys. 120, 11133 (2004)], (b) a polarizable and classically flexible molecule [H. Saint-Martin, J. Hernandez-Cobos, M. I. Bernal-Uruchurtu, I. Ortega-Blake, and H. J. C. Berendsen, J. Chem. Phys. 113, 10899 (2000)], (c) a polarizable and rigid molecule, and finally (d) a nonpolarizable and rigid molecule. The goal is to determine how significant the different molecular properties are. The results indicate that all factors--nonadditivity, polarizability, and intramolecular flexibility--are important. Still, approximations can be made in order to diminish the computational cost of the simulations with a small decrease in the accuracy of the predictions, provided that those approximations are counterbalanced by the proper inclusion of an effective molecular property, that is, an average molecular geometry or an average dipole. Hence instead of building an effective force field by parametrizing it in order to reproduce the properties of a specific phase, a building approach is proposed that is based on adequately restricting the molecular flexibility and/or polarizability of a model potential fitted to unimolecular properties, pair interactions, and many-body nonadditive contributions. In this manner, the same parental model can be used to simulate the same substance under a wide range of thermodynamic conditions. An additional advantage of this approach is that, as the force field improves by the quality of the molecular calculations, all levels of modeling can be improved.     

First hyperpolarizability of polymethineimine with long-range corrected functionals

Using the long-range corrected (LC) density functional theory (DFT) scheme introduced by Iikura et al. [J. Chem. Phys. 115, 3540 (2001)] and the Coulomb-attenuating model (CAM-B3LYP) of Yanai et al. [Chem. Phys. Lett. 393, 51 (2004)], we have calculated the longitudinal dipole moments and static electronic first hyperpolarizabilities of increasingly long polymehtineimine oligomers. For comparison purposes Hartree-Fock (HF), Moller-Plesset perturbation theory (MP2), and conventional pure and hybrid functionals have been considered as well. HF, generalized gradient approximation (GGA), and conventional hybrids provide too large dipole moments for long oligomers, while LC-DFT allows to reduce the discrepancy with respect to MP2 by a factor of 3. For the first hyperpolarizability, the incorrect evolution with the chain length predicted by HF is strongly worsened by BLYP, Perdew-Burke-Ernzerhof (PBE), and also by B3LYP and PBE0. On the reverse, LC-BLYP and LC-PBE hyperpolarizabilities are correctly predicted to be positive (but for the two smallest chains). Indeed, for medium and long oligomers LC hyperpolarizabilities are slightly smaller than MP2 hyperpolarizabilities, as it should be. CAM-B3LYP also strongly improves the B3LYP results, though a bit less impressively for small chain lengths. The present study demonstrates the efficiency of long-range DFT, even in very pathological cases.     

Communication: Linear-expansion shooting techniques for accelerating self-consistent field convergence

Based on the corrected Hohenberg-Kohn-Sham total energy density functional [Y. A. Zhang and Y. A. Wang, J. Chem. Phys. 130, 144116 (2009)], we have developed two linear-expansion shooting techniques (LIST)- direct LIST (LISTd) and indirect LIST (LISTi), to accelerate the convergence of self-consistent field (SCF) calculations. Case studies show that overall LISTi is the most robust and efficient algorithm for accelerating SCF convergence, whereas LISTd is advantageous in the early stage of an SCF process. More importantly, LISTi outperforms Pulay's direct inversion in the iterative subspace (DIIS) [P. Pulay, J. Comput. Chem. 3, 556 (1982)] and its two recent improvements, energy-DIIS [K. N. Kudin, G. E. Scuseria, and E. Cance?s, J. Chem. Phys. 116, 8255 (2002)] and augmented Roothaan-Hall energy-DIIS [X. Hu and W. Yang, J. Chem. Phys. 132, 054109 (2010)].     

Accuracy of recent potential energy surfaces for the He-N2 interaction. I. Virial and bulk transport coefficients

A new exchange-Coulomb semiempirical model potential energy surface for the He-N2 interaction has been developed. Together with two recent high-level ab initio potential energy surfaces, it has been tested for the reliability of its predictions of second-virial coefficients and bulk transport phenomena in binary mixtures of He and N2. The agreement with the relevant available measurements is generally within experimental uncertainty for the exchange-Coulomb surface and the ab initio surface of Patel et al. [J. Chem. Phys. 119, 909 (2003)], but with slightly poorer agreement for the earlier ab initio surface of Hu and Thakkar [J. Chem. Phys. 104, 2541 (1996)].     

Ab initio potential energy surfaces, bound states, and electronic spectrum of the Ar-SH complex

New ab initio potential energy surfaces for the (2)Pi ground electronic state of the Ar-SH complex are presented, calculated at the RCCSD(T)/aug-cc-pV5Z level. Weakly bound rotation-vibration levels are calculated using coupled-channel methods that properly account for the coupling between the two electronic states. The resulting wave functions are analyzed and a new adiabatic approximation including spin-orbit coupling is proposed. The ground-state wave functions are combined with those obtained for the excited (2)Sigma(+) state [D. M. Hirst, R. J. Doyle, and S. R. Mackenzie, Phys. Chem. Chem. Phys. 6, 5463 (2004)] to produce transition dipole moments. Modeling the transition intensities as a combination of these dipole moments and calculated lifetime values [A. B. McCoy, J. Chem. Phys. 109, 170 (1998)] leads to a good representation of the experimental fluorescence excitation spectrum [M.-C. Yang, A. P. Salzberg, B.-C. Chang, C. C. Carter, and T. A. Miller, J. Chem. Phys. 98, 4301 (1993)].