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A new method called adaptive force matching (AFM) has been developed that is capable of producing high quality force fields for condensed phase simulations. This procedure involves the parametrization of force fields to reproduce ab initio forces obtained from condensed phase quantum-mechanics/molecular-mechanics (QM/MM) calculations. During the procedure, the MM part of the QM/MM is iteratively improved so as to approach ab initio quality. In this work, the AFM method has been tested to parametrize force fields for liquid water so that the resulting force fields reproduce forces calculated using the ab initio MP2 and the Kohn–Sham density functional theory with the Becke–Lee–Yang–Parr (BLYP) and Becke three-parameter LYP (B3LYP) exchange correlation functionals. The AFM force fields generated in this work are very simple to evaluate and are supported by most molecular dynamics (MD) codes. At the same time, the quality of the forces predicted by the AFM force fields rivals that of very expensive ab initio calculations and are found to successfully reproduce many experimental properties. The site-site radial distribution functions (RDFs) obtained from MD simulations using the force field generated from the BLYP functional through AFM compare favorably with the previously published RDFs from Car–Parrinello MD simulations with the same functional. Technical aspects of AFM such as the optimal QM cluster size, optimal basis set, and optimal QM method to be used with the AFM procedure are discussed in this paper. [ABSTRACT FROM AUTHOR]

It is a well recognized difficult task to simulate the vibrational dynamics of ices using the density functional theory (DFT), and there has thus been rather limited success in modelling the inelastic neutron scattering (INS) spectra for even the simplest structure of ice, ice Ih, particularly in the translational region below 400 cm-1. The reason is partly due to the complex nature of hydrogen bonding (H-bond) among water-water molecules which require considerable improvement of the quantum mechanical simulation methods, and partly owing to the randomness of protons in ice structures which often requires simulation of large super-lattices. In this report, we present the first series of successful simulation results for ice Ih using DFT methods. On the basis of the recent advancement in the DFT programs, we have achieved for the first time theoretical outcomes that not only reproduce the rotational frequencies between 500 to 1200 cm-1 for ice Ih, but also the two optic peaks at ∼240 and 320 cm-1 in the translational region of the INS spectra [J. C. Li, J. Chem. Phys 105, 6733 (1996)]. Besides, we have also investigated the impact of pairwise configurations of H2O molecules on the H-bond and found that different proton arrangements of pairwise H2O in the ice Ih crystal lattice could not alter the nature of H-bond as significantly as suggested in an early paper [J. C. Li and D. K. Ross, Nature (London) 365, 327 (1993)], i.e., reproducing the two experimental optic peaks do not need to invoke the two H-bonds as proposed in the previous model which led to considerable debates. The results of this work suggest that the observed optic peaks may be attributed to the coupling between the two bands of H-O stretching modes in H2O. The current computational work is expected to shed new light on the nature of the H-bonds in water, and in addition to offer a new approach towards probing the interaction between water and biomaterials for which H-bond is essential. [ABSTRACT FROM AUTHOR]

Using quantum mechanics (QM) and classical force-field based molecular dynamics (FF), we have calculated the principle shock Hugoniot curves for numerous amorphous polymers including poly[methyl methacrylate] (PMMA), poly[styrene], polycarbonate, as well as both the amorphous and crystalline forms of poly[ethylene]. In the FF calculations, we considered a non-reactive force field (i.e., polymer consistent FF). The QM calculations were performed with density functional theory (DFT) using dispersion corrected atom centered pseudopotentials. Overall, results obtained by DFT show much better agreement with available experimental data than classical force fields. In particular, DFT calculated Hugoniot curves for PMMA up to 74 GPa are in very good agreement with experimental data, where a preliminary study of chain fracture and association was also performed. Structure analysis calculations of the radius of gyration and carbon-carbon radial distribution function were also carried out to elucidate contraction of the polymer chains with increasing pressure. [ABSTRACT FROM AUTHOR]

Using quantum molecular dynamics simulations based on density functional theory including dispersion corrections (DFT-D), we have studied the thermophysical properties of liquid carbon monoxide and nitrogen (CO-N2) mixture under extreme conditions. Density functional theory (DFT) method significantly overestimates the pressure as compared to DFT-D. It is demonstrated that the van der Waals (vdW) interaction has a negative contribution to the pressure and tends to reduce the overestimation of the equilibrium volume. We also demonstrate that a negative slope of Hugoniot curve could possibly be caused by both the absorption of dissociation energy and the uncertainties in composition. As density and temperature increase along the Hoguniot curve, the system appears to undergo a continuous transition and provides for a much richer set of dissociation products. The influence of dissociated carbon and oxygen atoms on nitrogen molecules is also discussed. [ABSTRACT FROM AUTHOR]

In an effort to design efficient platform for siRNA delivery, we combine all atom classical and quantum simulations to study the binding of small interfering RNA (siRNA) by pristine single wall carbon nanotube (SWCNT). Our results show that siRNA strongly binds to SWCNT surface via unzipping its base-pairs and the propensity of unzipping increases with the increase in the diameter of the SWCNTs. The unzipping and subsequent wrapping events are initiated and driven by van der Waals interactions between the aromatic rings of siRNA nucleobases and the SWCNT surface. However, molecular dynamics (MD) simulations of double strand DNA (dsDNA) of the same sequence show that the dsDNA undergoes much less unzipping and wrapping on the SWCNT in the simulation time scale of 70 ns. This interesting difference is due to smaller interaction energy of thymidine of dsDNA with the SWCNT compared to that of uridine of siRNA, as calculated by dispersion corrected density functional theory (DFT) methods. After the optimal binding of siRNA to SWCNT, the complex is very stable which serves as one of the major mechanisms of siRNA delivery for biomedical applications. Since siRNA has to undergo unwinding process with the effect of RNA-induced silencing complex, our proposed delivery mechanism by SWCNT possesses potential advantages in achieving RNA interference. [ABSTRACT FROM AUTHOR]

A time-dependent wavepacket diffusion method is proposed to deal with charge transport in organic crystals. The electron-phonon interactions in both site energies and electronic couplings are incorporated by the time-dependent fluctuations which are generated from the corresponding spectral density functions. The numerical demonstrations reveal that the present approach predicts the consistent charge carrier dynamics with the rigorous quantum approaches. In addition, the diffusion coefficients obtained from the Marcus formula are well reproduced at the weak electronic coupling and high temperature limits. It is also found that the charge mobility feature of the crossover from the band-like to the hopping-type cannot be predicted from the fluctuations induced by the linear electron-phonon interactions with an Ohmic spectral density; however, it indeed appears as the electronic coupling fluctuation exponentially depends on the nuclear coordinates. Finally, it should be noted that although the present approach neglects the imaginary fluctuation, it essentially incorporates the coherent motion of the charge carrier and quantum effect of the phonon motion with a broad regime of the fluctuations for symmetric systems. Besides, the approach can easily be applied to systems having thousands of sites, which allows one to investigate charge transport in nanoscale organic crystals. [ABSTRACT FROM AUTHOR]

For a rigorous quantum simulation of nonadiabatic dynamics of electrons and nuclei, knowledge of not only the first-order but also the second-order nonadiabatic couplings (NACs) is required. Here, we propose a method to efficiently calculate the second-order NAC from time-dependent density functional theory (TDDFT), on the basis of the Casida ansatz adapted for the computation of first-order NAC, which has been justified in our previous work and can be shown to be valid for calculating second-order NAC between ground state and singly excited states within the Tamm-Dancoff approximation. Test calculations of the second-order NAC in the immediate vicinity of Jahn-Teller and Renner-Teller intersections show that calculation results from TDDFT, combined with modified linear response theory, agree well with the prediction from the Jahn-Teller/Renner-Teller models. Contrary to the diverging behavior of the first-order NAC near all types of intersection points, the Cartesian components of the second-order NAC are shown to be negligibly small near Renner-Teller glancing intersections, while they are significantly large near the Jahn-Teller conical intersections. Nevertheless, the components of the second-order NAC can cancel each other to a large extent in Jahn-Teller systems, indicating the background of neglecting the second-order NAC in practical dynamics simulations. On the other hand, it is shown that such a cancellation becomes less effective in an elliptic Jahn-Teller system and thus the role of second-order NAC needs to be evaluated in the rigorous framework. Our study shows that TDDFT is promising to provide accurate data of NAC for full quantum mechanical simulation of nonadiabatic processes. [ABSTRACT FROM AUTHOR]

We present a combination of time-dependent density functional theory with the quantum mechanical/molecular mechanical approach which can be applied to study nonadiabatic dynamical processes in molecular systems interacting with the environment. Our method is illustrated on the example of ultrafast excited state dynamics of indole in water. We compare the mechanisms of nonradiative relaxation and the electronic state lifetimes for isolated indole, indole in a sphere of classical water, and indole + 3H2O embedded in a classical water sphere. In the case of isolated indole, the initial excitation to the S2 electronic state is followed by an ultrafast internal conversion to the S1 state with a time constant of 17 fs. The S1 state is long living (>30 ps) and deactivates to the ground state along the N-H stretching coordinate. This deactivation mechanism remains unchanged for indole in a classical water sphere. However, the lifetimes of the S2 and S1 electronic states are extended. The inclusion of three explicit water molecules opens a new relaxation channel which involves the electron transfer to the solvent, leading eventually to the formation of a solvated electron. The relaxation to the ground state takes place on a time scale of 60 fs and contributes to the lowering of the fluorescence quantum yield. Our simulations demonstrate the importance of including explicit water molecules in the theoretical treatment of solvated systems. [ABSTRACT FROM AUTHOR]

We have studied substituent effects on the properties of the intramolecular hydrogen bond of some ortho-hydroxy Schiff bases using density functional theory (DFT) based first-principle molecular dynamics (FPMD) and path integral molecular dynamics. The studied compounds possess a strong intramolecular hydrogen bond (r(O···N) ≤ 2.6 Å), which can be tuned by substitution to either (i) enhance the basicity of the acceptor moiety by induction effects or (ii) decrease the hydrogen bond length through steric repulsion. DFT calculations and FPMD were employed to investigate structural and dynamical properties of the selected molecules, while quantum effects on the structural properties were assessed using path integral FPMD. The simulations were performed in vacuo and in the solid state to study the influence of the environment on the hydrogen bond and spectroscopic properties. We give computational support to the suggestion that induction effects are less effective to tune the intramolecular hydrogen bond properties of the discussed ortho-hydroxy Schiff bases than the steric or the environmental effects. [ABSTRACT FROM AUTHOR]

We present a plane wave basis set implementation for the calculation of electronic coupling matrix elements of electron transfer reactions within the framework of constrained density functional theory (CDFT). Following the work of Wu and Van Voorhis [J. Chem. Phys. 125, 164105 (2006)], the diabatic wavefunctions are approximated by the Kohn-Sham determinants obtained from CDFT calculations, and the coupling matrix element calculated by an efficient integration scheme. Our results for intermolecular electron transfer in small systems agree very well with high-level ab initio calculations based on generalized Mulliken-Hush theory, and with previous local basis set CDFT calculations. The effect of thermal fluctuations on the coupling matrix element is demonstrated for intramolecular electron transfer in the tetrathiafulvalene-diquinone (Q-TTF-Q-) anion. Sampling the electronic coupling along density functional based molecular dynamics trajectories, we find that thermal fluctuations, in particular the slow bending motion of the molecule, can lead to changes in the instantaneous electron transfer rate by more than an order of magnitude. The thermal average, (<|Hab|2>)1/2=6.7 mH, is significantly higher than the value obtained for the minimum energy structure, |Hab|=3.8 mH. While CDFT in combination with generalized gradient approximation (GGA) functionals describes the intermolecular electron transfer in the studied systems well, exact exchange is required for Q-TTF-Q- in order to obtain coupling matrix elements in agreement with experiment (3.9 mH). The implementation presented opens up the possibility to compute electronic coupling matrix elements for extended systems where donor, acceptor, and the environment are treated at the quantum mechanical (QM) level. [ABSTRACT FROM AUTHOR]

Using a recently implemented technique for the calculation of the adiabatic connection (AC) of density functional theory (DFT) based on Lieb maximization with respect to the external potential, the AC is studied for atoms and molecules containing up to ten electrons: the helium isoelectronic series, the hydrogen molecule, the beryllium isoelectronic series, the neon atom, and the water molecule. The calculation of AC curves by Lieb maximization at various levels of electronic-structure theory is discussed. For each system, the AC curve is calculated using Hartree–Fock (HF) theory, second-order Mo\ller–Plesset (MP2) theory, coupled-cluster singles-and-doubles (CCSD) theory, and coupled-cluster singles-doubles-perturbative-triples [CCSD(T)] theory, expanding the molecular orbitals and the effective external potential in large Gaussian basis sets. The HF AC curve includes a small correlation-energy contribution in the context of DFT, arising from orbital relaxation as the electron-electron interaction is switched on under the constraint that the wave function is always a single determinant. The MP2 and CCSD AC curves recover the bulk of the dynamical correlation energy and their shapes can be understood in terms of a simple energy model constructed from a consideration of the doubles-energy expression at different interaction strengths. Differentiation of this energy expression with respect to the interaction strength leads to a simple two-parameter doubles model (AC-D) for the AC integrand (and hence the correlation energy of DFT) as a function of the interaction strength. The structure of the triples-energy contribution is considered in a similar fashion, leading to a quadratic model for the triples correction to the AC curve (AC-T). From a consideration of the structure of a two-level configuration-interaction (CI) energy expression of the hydrogen molecule, a simple two-parameter CI model (AC-CI) is proposed to account for the effects of static correlation on the AC. When parametrized in terms of the same input data, the AC-CI model offers improved performance over the corresponding AC-D model, which is shown to be the lowest-order contribution to the AC-CI model. The utility of the accurately calculated AC curves for the analysis of standard density functionals is demonstrated for the BLYP exchange-correlation functional and the interaction-strength-interpolation (ISI) model AC integrand. From the results of this analysis, we investigate the performance of our proposed two-parameter AC-D and AC-CI models when a simple density functional for the AC at infinite interaction strength is employed in place of information at the fully interacting point. The resulting two-parameter correlation functionals offer a qualitatively correct behavior of the AC integrand with much improved accuracy over previous attempts. The AC integrands in the present work are recommended as a basis for further work, generating functionals that avoid spurious error cancellations between exchange and correlation energies and give good accuracy for the range of densities and types of correlation contained in the systems studied here. [ABSTRACT FROM AUTHOR]

We present a plane-wave basis set implementation of charge constrained density functional molecular dynamics (CDFT-MD) for simulation of electron transfer reactions in condensed phase systems. Following the earlier work of Wu and Van Voorhis [Phys. Rev. A 72, 024502 (2005)], the density functional is minimized under the constraint that the charge difference between donor and acceptor is equal to a given value. The classical ion dynamics is propagated on the Born–Oppenheimer surface of the charge constrained state. We investigate the dependence of the constrained energy and of the energy gap on the definition of the charge and present expressions for the constraint forces. The method is applied to the Ru2+–Ru3+ electron self-exchange reaction in aqueous solution. Sampling the vertical energy gap along CDFT-MD trajectories and correcting for finite size effects, a reorganization free energy of 1.6 eV is obtained. This is 0.1-0.2 eV lower than a previous estimate based on a continuum model for solvation. The smaller value for the reorganization free energy can be explained by the fact that the Ru–O distances of the divalent and trivalent Ru hexahydrates are predicted to be more similar in the electron transfer complex than for the separated aqua ions. [ABSTRACT FROM AUTHOR]

A quantum mechanics/molecular mechanics (QM/MM) type of scheme is employed to calculate the solvent-induced shifts of molecular electronic excitations. The effective fragment potential (EFP) method was used for the classical potential. Since EFP has a density dependent functional form, in contrast with most other MM potentials, time-dependent density functional theory (TDDFT) has been modified to combine TDDFT with EFP. This new method is then used to perform a hybrid QM/MM molecular dynamics simulation to generate a simulated spectrum of the n→π* vertical excitation energy of acetone in vacuum and with 100 water molecules. The calculated water solvent effect on the vertical excitation energy exhibits a blueshift of the n→π* vertical excitation energy in acetone (Δω1=0.211 eV), which is in good agreement with the experimental blueshift. [ABSTRACT FROM AUTHOR]

The structural properties of liquid GeSe2, generated using two distinct computational methodologies, are compared. The results of molecular dynamics simulations, utilizing both first-principles density functional and a potential model which account for aspects of many-body interactions, are considered. The potential model favors ionic character in the bonding, resulting in a structure with very little chemical disorder and no homopolar bonds, in contrast to experimental observation. The use of a relatively simple potential model is shown to be useful in order to understand differences between the observed experimental structure and those obtained from the first-principles approach, the latter being affected by insufficient account of ionic character in the bonding. Both computational schemes are able to predict the appearance of the first sharp diffraction peak in the total neutron structure factor and in some of the partial structure factors as well as the concomitant presence of corner- and edge-sharing tetrahedral connections. For the potential model, this holds true provided the system temperatures are set to values high enough to allow for diffusion properties typical of a liquid. Structural properties obtained for the two sets of configurations are in closer agreement when the potential model is applied at very high temperatures. [ABSTRACT FROM AUTHOR]

Absorption spectra of silane in the region of the first overtone of the Si–H stretch vibration have been recorded in a seeded supersonic jet expansion by cavity ring-down spectroscopy as well as in a static gas cell at room temperature by photoacoustic spectroscopy. Spectral simplification due to strong rotational cooling in the jet expansion enables us to clearly resolve and assign the rovibrational transitions of the (2000) and (1100) bands of the three isotopologues, 28SiH4, 29SiH4, and 30SiH4, in their natural isotopic abundance. Interconversion between different nuclear spin species of SiH4 is found to be absent during the jet expansion. Isotope shifts for 29SiH4 and 30SiH4 relative to 28SiH4 are measured and found to be suitable for selective vibrational excitation of any of three silane isotopologues by pulsed laser excitation in a jet expansion. [ABSTRACT FROM AUTHOR]

We present a library of Gaussian basis sets that has been specifically optimized to perform accurate molecular calculations based on density functional theory. It targets a wide range of chemical environments, including the gas phase, interfaces, and the condensed phase. These generally contracted basis sets, which include diffuse primitives, are obtained minimizing a linear combination of the total energy and the condition number of the overlap matrix for a set of molecules with respect to the exponents and contraction coefficients of the full basis. Typically, for a given accuracy in the total energy, significantly fewer basis functions are needed in this scheme than in the usual split valence scheme, leading to a speedup for systems where the computational cost is dominated by diagonalization. More importantly, binding energies of hydrogen bonded complexes are of similar quality as the ones obtained with augmented basis sets, i.e., have a small (down to 0.2 kcal/mol) basis set superposition error, and the monomers have dipoles within 0.1 D of the basis set limit. However, contrary to typical augmented basis sets, there are no near linear dependencies in the basis, so that the overlap matrix is always well conditioned, also, in the condensed phase. The basis can therefore be used in first principles molecular dynamics simulations and is well suited for linear scaling calculations. [ABSTRACT FROM AUTHOR]

The analysis of previously reported shortcomings of the condensed Fukui functions obtained making use of the quantum theory of atoms in molecules indicates these drawbacks are due to the inadequacy of the definition employed to compute them and not to the partitioning. A new procedure, which respects the mathematical definition and solves these problems, is presented for the calculation of condensed Fukui functions for atomic basins defined according to the quantum theory of atoms in molecules. It is tested in a set of 18 molecules, which includes the most controversial reported cases. [ABSTRACT FROM AUTHOR]

The Gaussian-4 theory (G4 theory) for the calculation of energies of compounds containing first- (Li–F), second- (Na–Cl), and third-row main group (K, Ca, and Ga–Kr) atoms is presented. This theoretical procedure is the fourth in the Gaussian-n series of quantum chemical methods based on a sequence of single point energy calculations. The G4 theory modifies the Gaussian-3 (G3) theory in five ways. First, an extrapolation procedure is used to obtain the Hartree-Fock limit for inclusion in the total energy calculation. Second, the d-polarization sets are increased to 3d on the first-row atoms and to 4d on the second-row atoms, with reoptimization of the exponents for the latter. Third, the QCISD(T) method is replaced by the CCSD(T) method for the highest level of correlation treatment. Fourth, optimized geometries and zero-point energies are obtained with the B3LYP density functional. Fifth, two new higher level corrections are added to account for deficiencies in the energy calculations. The new method is assessed on the 454 experimental energies in the G3/05 test set [L. A. Curtiss, P. C. Redfern, and K. Raghavachari, J. Chem. Phys. 123, 124107 (2005)], and the average absolute deviation from experiment shows significant improvement from 1.13 kcal/mol (G3 theory) to 0.83 kcal/mol (G4 theory). The largest improvement is found for 79 nonhydrogen systems (2.10 kcal/mol for G3 versus 1.13 kcal/mol for G4). The contributions of the new features to this improvement are analyzed and the performance on different types of energies is discussed. [ABSTRACT FROM AUTHOR]

In order to better understand the physical interactions that stabilize protein secondary structure, the neat liquid state of a peptidic fragment, N-methylacetamide (NMA), was studied using computer simulation. Three different descriptions of the molecular liquid were examined: an empirical force field treatment with classical nuclei, an empirical force field treatment with quantum mechanical nuclei, and an ab initio density functional theory (DFT) treatment. The DFT electronic structure was evaluated using the BLYP approximate functional and a plane wave basis set. The different physical effects probed by the three models, such as quantum dispersion, many-body polarization, and nontrivial charge distributions on the liquid properties, were compared. Much of the structural ordering in the liquid is characterized by hydrogen bonded chains of NMA molecules. Modest structural differences are present among the three models of liquid NMA. The average molecular dipole in the liquid under the ab initio treatment, however, is enhanced by 60% over the gas phase value. [ABSTRACT FROM AUTHOR]

A series of 20 ps ab initio molecular dynamics simulations of water at ambient density and temperatures ranging from 300 to 450 K are presented. Car-Parrinello (CP) and Born-Oppenheimer (BO) molecular dynamics techniques are compared for systems containing 54 and 64 water molecules. At 300 K, an excellent agreement is found between radial distribution functions (RDFs) obtained with BO and CP dynamics, provided an appropriately small value of the fictitious mass parameter is used in the CP simulation. However, we find that the diffusion coefficients computed from CP dynamics are approximately two times larger than those obtained with BO simulations for T>400 K, where statistically meaningful comparisons can be made. Overall, both BO and CP dynamics at 300 K yield overstructured RDFs and slow diffusion as compared to experiment. In order to understand these discrepancies, the effect of proton quantum motion is investigated with the use of empirical interaction potentials. We find that proton quantum effects may have a larger impact than previously thought on structure and diffusion of the liquid. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

A new formalism for quantum functional sensitivity analysis (QFSA) of atom–diatom reactions in the gas phase is developed within a version of Manolopoulos et al.’s [J. Chem. Phys. 93, 403 (1990)] log-derivative Kohn variational method containing contracted translational basis functions. A reference energy, Emid, is introduced to define boundary translational functions which completely remove all scattering energy dependence from the basis functions. This greatly facilitates scattering calculations for a range of energies about Emid without having to recalculate any of the so-called ‘‘stiffness’’ matrix elements. Our new approach to QFSA is applied to study the sensitivity of the H+H2, D+H2, and H+D2 reaction probabilities to the Boothroyd–Keogh–Martin–Peterson (BKMP) potential energy surface. The transition probability sensitivities of both D+H2 and H+D2 are very similar to those of H+H2 at low energies, but at higher energies, the sensitivities of the H+D2 reaction differ from those of the other two isotopomers. Isotopomers that have very similar reaction probability profiles also have very similar sensitivities to the potential. All three isotopomers exhibit a large region of positive sensitivity at the top of the barrier for an approximately 0.1 to 0.2 eV energy range above threshold. For these energies (∼0.3 to 0.5 eV above the barrier), it is possible to increase the reaction probability with slight increases in barrier height. Sensitivity results from our new code have also provided a wealth of information about (i) how small, localized changes in the potential affect product state distributions, resonance features, and reactivity; and (ii) where the dynamics is most sensitive to inaccuracies in the potential. Comparisons are also made of transition probabilities and sensitivities on the BKMP surface to those of other potential energy surfaces. © 1995 American Institute of Physics. [ABSTRACT FROM AUTHOR]