Geometry Relaxation Effects Research Articles

Calculation of the geometry, absorption spectrum, and first hyperpolarizability of 4,5-dicyanoimidazole derivatives in solution. A multiscale ASEC-FEG study.

We investigate the effects of solvents on the geometry, absorption spectrum, and first hyperpolarizability of six push-pull molecules, each containing a 4,5-dicyanoimidazole group as an electron acceptor and a N,N-dimethylamino group as an electron donor, with systematically extended π-conjugated systems. Geometry optimizations in dichloromethane, methanol, water, and formamide under normal thermodynamic conditions were performed using the average solvent electrostatic configuration-free energy gradient method, which employs a discrete solvent model. The conformational structure of molecules is moderately affected by the environment, with the π-conjugated system becoming more planar in protic solvents. Solvent effects on the first hyperpolarizability result in marked increases that are in line with the red shifts of the absorption spectrum. The hyperpolarizability of smaller molecules within the set may be significantly influenced by the effects of geometry relaxation in highly polar protic solvents. The results illustrate the role of hydrogen bonds in the structure and electronic properties of push-pull molecules in protic environments. For smaller molecules, hydrogen bonds significantly contribute to enhancing the hyperpolarizability, but the effect of these specific interactions becomes less significant with the length of the π-conjugated system.

Stability of topological properties of bismuth (1 1 1) bilayer

We investigate the electronic and transport properties of the bismuth (1 1 1) bilayer in the context of the stability of its topological properties against different perturbations. The effects of spin–orbit coupling variations, geometry relaxation and interaction with a substrate are considered. The transport properties are studied in the presence of Anderson disorder. Band structure calculations are performed within the multi-orbital tight-binding model and density functional theory methods. A band inversion process in the bismuth (1 1 1) infinite bilayer and an evolution of the edge state dispersion in ribbons as a function of spin–orbit coupling strength are analyzed. A significant change in the orbital composition of the conduction and valence bands is observed during a topological phase transition. The topological edge states are shown to be weakly affected by the effect of ribbon geometry relaxation. The interaction with a substrate is considered for narrow ribbons on top of another bismuth (1 1 1) bilayer. This corresponds to a weakly interacting case and the effect is similar to an external perpendicular electric field. Robust quantized conductance is observed when the Fermi energy lies within the energy gap, where only two counter-propagating edge states are present. For energies where the Fermi level crosses more in-gap states, scattering is possible between the channels lying close in the k-space. When the energy of the edge states overlaps the valence states, no topological protection is observed.

Artificial neural network for the configuration problem in solids.

A machine learning approach based on the artificial neural network (ANN) is applied for the configuration problem in solids. The proposed method provides a direct mapping from configuration vectors to energies. The benchmark conducted for the M1 phase of Mo-V-Te-Nb oxide showed that only a fraction of configurations needs to be calculated, thus the computational burden significantly decreased, by a factor of 20-50, with R2 = 0.96 and MAD = 0.12 eV. It is shown that ANN can also handle the effects of geometry relaxation when properly trained, resulting in R2 = 0.95 and MAD = 0.13 eV.

Ground-state dipole moment of the spatially confined carbon monoxide and boron fluoride molecules

In this contribution the influence of spatial confinement on the dipole moment of carbon monoxide and boron fluoride was investigated. The spatial confinement was modeled by applying the two-dimensional harmonic oscillator potential. The dipole moment calculations were performed for both molecules using their experimental geometries and also including the effect of geometry relaxation in the presence of confining potential. Our results demonstrate that the dipole moment is noticeably affected by the confinement. Moreover, it was found that the changes in the dipole moment, caused by the presence of harmonic oscillator potential, are substantially different for each of the studied molecules.

Electric properties of the low-lying excited states of benzonitrile: geometry relaxation and solvent effects

Accurate calculations of the dipole moment and the polarizability for the ground and two lowest singlet and triplet excited states of benzonitrile (BN) have been performed by a variety of wave function and density functional theory (DFT) methods. Changes in molecular properties upon the electron excitation strongly depend on the character of an excited state. The vertical dipole moment change and the excess polarizability for the 11B state are smaller than those for the 21A state. In order to estimate adiabatic excited-state properties, corresponding relaxed geometries have been obtained using the PBE0 functional with the aug-cc-pVTZ basis set. The excited-state property values obtained with the long-range exchange corrected DFT methods are in general closer to the coupled cluster (CC) results, although the hybrid DFTs also provide reasonable predictions. Our CCSD adiabatic excess dipole moment value for the 11B state equal to 0.11 D is in excellent agreement with the experimental value. The 21A state appears to be more sensitive to selected method due to an important role of double-excitation effects. Solvent effects on dipole moment and polarizability of BN molecule in its ground and excited states were evaluated using both LR and cLR methods combined with the (TD-)CAMB3LYP/POL approach.

Ab initio Variational Transition State Theory and Master Equation Study of the Reaction (OH)3SiOCH2 + CH3 ⇌ (OH)3SiOC2H5

Abstract In this paper we use variable reaction coordinate variational transition state theory (VRC-TST) to calculate the reaction rate constants for the two reactions, R1: (OH)3SiOCH2 + CH3 ⇌ (OH)3SiOC2H5, and R2: CH2OH + CH3 ⇌ C2H5OH. The first reaction is an important channel during the thermal decomposition of tetraethoxysilane (TEOS), and its rate coefficient is the main focus of this work. The second reaction is analogous to the first and is used as a basis for comparison. The interaction energies are obtained on-the-fly at the CASPT2(2e,2o)/cc-pVDZ level of theory. A one-dimensional correction to the sampled energies was introduced to account for the energetic effects of geometry relaxation along the reaction path. The computed, high-pressure rate coefficients were calculated to be, R1: k 1 = 2.406 × 10−10 T −0.301 exp (− 271.4/T) cm3 molecule –1 s –1 and R2: k 2 = 1.316 × 10−10 T −0.189 exp (− 256.5/T) cm3 molecule –1 s –1. These rates differ from each other by only 10% – 30% over the temperature range 300–2000 K. A comparison of the computed rates with experimental data shows good agreement and an improvement over previous results. The pressure dependency of the reaction R1 is explored by solving a master equation using helium as a bath gas. The results obtained show that the reaction is only weakly pressure dependent over the temperature range 300–1700 K, with the predicted rate constant being within 50% of its high-pressure limit at atmospheric pressure.

A Theoretical Study of the Formation of Benzene Excimer: Effects of Geometry Relaxation and Spin-state Dependence

Geometry relaxation effects on the formation of benzene excimer were investigated by means of ab initio calculation at SOS-CIS(D0)/aug-cc-pVDZ level. In the case of T-shaped dimer configuration, intermolecular interactions in the excited states are found to be nearly the same as those in the ground state and structural deformations are limited within a single molecule; the geometry relaxation effects are then negligible and singlet-triplet energy gap remains constant. As for face-to-face eclipsed dimer, on the other hand, both molecules undergo structural change. As a result, intermolecular interactions in the excited states are significantly different than those in the ground state. Although the intermolecular distances obtained from potential energy curve calculation with frozen molecular structures are in qualitative agreement, the excitedstate binding energies are notably overestimated with respect to those at optimized structures. In particular, the effects are calculated to be larger in T1 state and hence singlet-triplet energy gap, which reduces markedly in this configuration, is underestimated without relaxation.

Communication: Determining the lowest-energy isomer of Au8: 2D, or not 2D

A parallel numerical derivative code, combined with parallel implementation of the coupled-cluster method with singles, doubles, and non-iterative triples (CCSD(T)), is used to optimize the geometries of the low-energy structures of the Au8 particle. The effects of geometry relaxation at the CCSD(T) level and the combined effects of the basis set and core-valence correlations are examined and the results are compared with the corresponding second-order Møller-Plesset perturbation theory calculations. The highest-level computations, in which the single-point CCSD(T) calculations employing the correlation-consistent basis set of the cc-pVTZ quality and the associated relativistic effective core potential (ECP), both optimized for gold, and correlating the 5d(10)6s(1) valence and 5s(2)5p(6) semi-core electrons, are combined with the geometrical information obtained with the corresponding CCSD(T)/cc-pVDZ/ECP approach, favor the planar configuration, with the next three non-planar structures separated by 4-6 kcal/mol. In agreement with the earlier work, smaller-basis set CCSD(T) computations provide unreliable results for the relative energetics, even when the geometries are optimized at the CCSD(T) level.

Electronically Excited States in Poly(p-phenylenevinylene): Vertical Excitations and Torsional Potentials from High-Level Ab Initio Calculations

Ab initio second-order algebraic diagrammatic construction (ADC(2)) calculations using the resolution of the identity (RI) method have been performed on poly-(p-phenylenevinylene) (PPV) oligomers with chain lengths up to eight phenyl rings. Vertical excitation energies for the four lowest π–π* excitations and geometry relaxation effects for the lowest excited state (S1) are reported. Extrapolation to infinite chain length shows good agreement with analogous data derived from experiment. Analysis of the bond length alternation (BLA) based on the optimized S1 geometry provides conclusive evidence for the localization of the defect in the center of the oligomer chain. Torsional potentials have been computed for the four excited states investigated and the transition densities divided into fragment contributions have been used to identify excitonic interactions. The present investigation provides benchmark results, which can be used (i) as reference for lower level methods and (ii) give the possibility to parametrize an effective Frenkel exciton Hamiltonian for quantum dynamical simulations of ultrafast exciton transfer dynamics in PPV type systems.

Effect of nucleobase sequence on the proton-transfer reaction and stability of the guanine–cytosine base pair radical anion

The formation of base pair radical anions is closely related to many fascinating research fields in biology and chemistry such as radiation damage to DNA and electron transport in DNA. However, the relevant knowledge so far mainly comes from studies on isolated base pair radical anions, and their behavior in the DNA environment is less understood. In this study, we focus on how the nucleobase sequence affects the properties of the guanine-cytosine (GC) base pair radical anion. The energetic barrier and reaction energy for the proton transfer along the N(1)(G)-H···N(3)(C) hydrogen bond and the stability of GC˙(-) (i.e., electron affinity of GC) embedded in different sequences of base-pair trimer were evaluated using density functional theory. The computational results demonstrated that the presence of neighboring base pairs has an important influence on the behavior of GC˙(-) in the gas phase. The excess electron was found to be localized on the embedded GC and the charge leakage to neighboring base pairs was very minor in all of the investigated sequences. Accordingly, the sequence behavior of the proton-transfer reaction and the stability of GC˙(-) is chiefly governed by electrostatic interactions with adjacent base pairs. However, the effect of base stacking, due to its electrostatic nature, is severely screened upon hydration, and thus, the sequence dependence of the properties of GC˙(-) in aqueous environment becomes relatively weak and less than that observed in the gas phase. The effect of geometry relaxation associated with neighboring base pairs as well as the possibility of proton transfer along the N(2)(G)-H···O(2)(C) channel have also been investigated. The implications of the present findings to the electron transport and radiation damage of DNA are discussed.

NMR Chemical Shielding and Spin−Spin Coupling Constants of Liquid NH3: A Systematic Investigation using the Sequential QM/MM Method

The NMR spin coupling parameters, (1)J(N,H) and (2)J(H,H), and the chemical shielding, sigma((15)N), of liquid ammonia are studied from a combined and sequential QM/MM methodology. Monte Carlo simulations are performed to generate statistically uncorrelated configurations that are submitted to density functional theory calculations. Two different Lennard-Jones potentials are used in the liquid simulations. Electronic polarization is included in these two potentials via an iterative procedure with and without geometry relaxation, and the influence on the calculated properties are analyzed. B3LYP/aug-cc-pVTZ-J calculations were used to compute the (1)J(N,H) constants in the interval of -67.8 to -63.9 Hz, depending on the theoretical model used. These can be compared with the experimental results of -61.6 Hz. For the (2)J(H,H) coupling the theoretical results vary between -10.6 to -13.01 Hz. The indirect experimental result derived from partially deuterated liquid is -11.1 Hz. Inclusion of explicit hydrogen bonded molecules gives a small but important contribution. The vapor-to-liquid shifts are also considered. This shift is calculated to be negligible for (1)J(N,H) in agreement with experiment. This is rationalized as a cancellation of the geometry relaxation and pure solvent effects. For the chemical shielding, sigma((15)N) calculations at the B3LYP/aug-pcS-3 show that the vapor-to-liquid chemical shift requires the explicit use of solvent molecules. Considering only one ammonia molecule in an electrostatic embedding gives a wrong sign for the chemical shift that is corrected only with the use of explicit additional molecules. The best result calculated for the vapor to liquid chemical shift Delta sigma((15)N) is -25.2 ppm, in good agreement with the experimental value of -22.6 ppm.

Dissecting the Hindered Rotation of Ethane

The existence of a rotational barrier of ca. 3 kcalmol 1 around the C C single bond in ethane has been known since the early studies of Ebert, Wagner, Eucken and Weigert and Pitzer done in the 1930s. Even the simplest ab initio methods are able to reproduce this fundamental result. However, the physical origin of this hindered rotation is still under controversy in the literature. There are two effects that have been regarded as responsible for the rotational barrier : a larger steric repulsion in the eclipsed conformation and an enhanced stabilization of the staggered conformation due to hyperconjugation. Clearly, the two effects (and possibly some other ones) coexist in ethane, so in order to quantify the magnitude of one of them one must be able to switch off the other in the model calculation. The steric repulsion still remains the most popular explanation of the hindered rotation of ethane. This effect is often understood as the increase in energy that accompanies the antisymmetrization of a wave function originally formed by strictly localized descriptions of two methyl groups brought up to the final ethane geometry where they overlap. This so-called Pauli repulsion is considered to be more important for the eclipsed conformation, where the overlap between the occupied sC H molecular orbitals is larger, thus giving rise to a hindered rotation. The non-orthogonality between the molecular orbitals (MOs) of the two fragments seems to be the main source of controversy of such models. It has been argued that a zerothorder unperturbed system formed by two non-orthogonal sets cannot be put in correspondence with a Hermitian Hamiltonian, raising doubts about any physical argument obtained from a perturbative approach using such a model. (We cannot accept this point of view, which would exclude all the perturbation theories of intermolecular interactions as being illegitimate.) The hyperconjugation effect is due to interactions/delocalizations between electrons of vicinal C H bonds mainly through the C C bond. In an MO picture, this corresponds to favorable two-electron two-orbital interactions between the occupied sC H orbital of one methyl group and the virtual antibonding s*C H orbital of the other. This also involves orbital s*C C. [21] The electron delocalization effect can easily be assessed in valence bond (VB) theory calculations by adding/ removing the appropriate resonance structures from the wave function. In an MO calculation it is not that simple due to the delocalized nature of the MOs. The hyperconjugation effect is estimated by constructing the wave function from sets of MOs localized in methyl moieties. The way such MOs are constructed, in particular whether they are variationally optimized, apparently led to opposite conclusions about the role of the hyperconjugation in the rotational barrier. Another factor to be taken into account is the geometry relaxation that accompanies the internal rotation, and in particular the change in the C C distance. It is somewhat striking that the C C bond is significantly shorter in the staggered conformation than in the eclipsed one although this bond is formally not changing during the rotation. This effect already appears at the simplest minimal basis SCF level of theory: at the STO6G level one gets C C bond lengths equal to 1.535 and 1.545 , respectively. At the same time the effect of geometry relaxation on the height of the barrier is minor. Nonetheless, previous studies concluded that different answers can be obtained for the relative importance of the steric repulsion and the hyperconjugation effect depending on whether the geometry relaxation has been considered or not. Previous energy decomposition analyses relied, in one way or another, on the definition of two methyl fragments. However, in the last years there have been a growing interest in other kinds of energy partitioning schemes, closely related to population analysis and bond-order techniques. Such schemes allow expressing the total energy of a system, exactly or up to a good accuracy, as a sum of atomic and diatomic contributions, as given by Equation (1):

Effects of field-induced geometry relaxation on the electron transport properties of 4,4′-biphenyldithiol molecular junction

The non-linear charge transport properties of 4,4′-biphenyldithiol molecular junction have been studied using the generalized Green’s function theory. It is shown that the torsion angle between two phenyls is slightly decreased as increase of the external voltage while the whole molecule moves slightly along the reversed direction of the electric field. Calculations indicate that the inclusion of molecular geometry relaxation can avoid a false prediction of negative differential resistance behavior. The charge redistribution under the external bias results in resistive dipoles inside the molecule. The calculated I– V curves of 4,4′-biphenyldithiol molecular junction is consistent with experimental observations in some ways.

UV-vis spectra of p-benzoquinone anion radical in solution by a TD-DFT/PCM approach

Excited electronic states of the anion radical of para-benzoquinone were studied by time dependent density functional theory (TD-DFT) including bulk solvent effects by the polarizable continuum model (PCM). The computed vertical excitation energies for the first four low-lying doublet states are in good agreement with previous post-Hartree–Fock computations. Geometry optimization of excited states and inclusion of solvent effects lead to a remarkable agreement between computed adiabatic transition energies and experimental band maxima. Together with their specific interest, the results point out the reliability of TD-DFT/PCM approach for valence excitations and the need to take geometry relaxation and solvent effects into the proper account for a meaningful comparison between computed and experimental absorption spectra.

Excited‐State Properties and Environmental Effects for Protonated Schiff Bases: A Theoretical Study

Complete active space self-consistent field (CASSCF), multireference configuration interaction (MRCI), density functional theory (DFT), time dependent DFT (TDDFT) and the singles and doubles coupled-cluster (CC2) methodologies have been used to study the ground state and excited states of protonated and neutral Schiff bases (PSB and SB) as models for the retinal chromophore. Systems with two to four conjugated double bonds are investigated. Geometry relaxation effects are studied in the excited pipi* state using the aforementioned methods. Taking the MRCI results as reference we find that CASSCF results are quite reliable even though overshooting of geometry changes is observed. TDDFT does not reproduce bond alternation well in the pipi* state. CC2 takes an intermediate position. Environmental effects due to solvent or protein surroundings have been studied in the excited states of the PSBs and SBs using a water molecule and solvated formate as model cases. Particular emphasis is given to the proton transfer process from the PSB to its solvent partner in the excited state. It is found that its feasibility is significantly enhanced in the excited state as compared to the ground state, which means that a proton transfer could be initiated already at an early step in the photodynamics of PSBs.

Symmetry-dependent vibrational excitation in N 1s photoionization of N2: Experiment and theory

We have measured the vibrational structures of the N 1s photoelectron mainline and satellites of the gaseous N2 molecule with the resolution better than 75 meV. The gerade and ungerade symmetries of the core-ionized (mainline) states are resolved energetically, and symmetry-dependent angular distributions for the satellite emission allow us to resolve the Sigma and Pi symmetries of the shake-up (satellite) states. Symmetry-adapted cluster-expansion configuration-interaction calculations of the potential energy curves for the mainline and satellite states along with a Franck-Condon analysis well reproduce the observed vibrational excitation of the bands, illustrating that the theoretical calculations well predict the symmetry-dependent geometry relaxation effects. The energies of both mainline states and satellite states, as well as the splitting between the mainline gerade and ungerade states, are also well reproduced by the calculation: the splitting between the satellite gerade and ungerade states is calculated to be smaller than the experimental detection limit.

Geometry relaxation in the excited states and its effects on the electronic properties of the Er(8-hydroxyquinolate)3 complex

Abstract We present the results of a semiempirical study of the geometry relaxation effects on the electronic properties of the Er(8-hydroxyquinolinate)3 complex, chosen as a model system in which energy transfer takes place. Geometry distortion in the excited states can affect several photophysical properties such as Stokes shifts, emission in target regions of the spectrum, lifetimes and others. In spite of this fact, in the majority of the theoretical works geometry rearrangements induced by photon absorption are simply ignored, due also to practical difficulties connected to the size of the complexes. In this paper we will use a simple semiempirical approach for the theoretical calculation of the excitation energies of the organic part of the complex, and we will show that the explicit consideration of the geometrical relaxation allows to identify (at least in this case) the most energetically favourable channel for the population of the triplet state.

Second-harmonic generation of solvated molecules using multiconfigurational self-consistent-field quadratic response theory and the polarizable continuum model

We present the first implementation of the quadratic response function for multiconfigurational self-consistent-field wave functions of solvated molecules described by a polarizable continuum model employing a molecule-shaped cavity. We apply the methodology to the first hyperpolarizability beta and, in particular, the second-harmonic generation process for a series of conjugated push-pull oligomers, as well as for para-nitroaniline. The effect of solvation on the dispersion of the hyperpolarizability and the change in the hyperpolarizability for increasing chain length of the oligomers in vacuum and in solution is considered. The effect of a correlated description is analyzed by comparing the Hartree-Fock hyperpolarizabilities to the multiconfigurational self-consistent-field hyperpolarizabilities. The effect of geometry relaxation in the solvent on the properties of the solvated molecules are also investigated.

Semiempirical Study of the Electronic and Optical Properties of the Er(8-hydroxyquinolinate)3 Complex

We use a simple quantum chemical semiempirical procedure to study the electronic properties of organic-lanthanide complexes, taking as a model system Er(8-hydroxyquinolinate)3. Among the problems inherent to such a study is the fact that the lanthanide ion has never been parametrized in any of the standard semiempirical Hamiltonians. To overcome this difficulty, the lanthanide ion is replaced by a different but somewhat similar parametrized ion, or merely by a point charge. Good agreement with experiment, where available, is obtained, particularly in the former case. In fact, the electronic properties of the complex (apart from the emission properties) are seen to be scarcely affected by the nature of the lanthanide ion itself, but the core interactions between the metal ion and the ligand units play a relevant role, also in the calculation of the excitation energies. In particular, the ordering and separation of both singlet and triplet excited states are affected. The main conclusion is that to describe in detail the mechanism of the energy-transfer process occurring in the complex it is essential to take into account the geometry relaxation effects in the excited states.

Electronic correlations in oligo-thiophene molecular crystals

The Coulomb interaction between two holes on oligo-thiophene molecules is studied systematically as a function of the oligomer length using first principles density function calculations. The effect of molecular geometry relaxation upon this interaction is found to be small. In contrast, electronic polarization of the molecules that surround the charged oligomer in the crystal lattice reduces the bare Coulomb repulsion between the holes by approximately a factor of 2. In all cases, the effective hole–hole repulsion is much larger than the valence band width, which means that at high doping levels, strong correlation effects should become important.