Molecular Orbital Configuration Interaction Research Articles

Excited state free energy calculations of Cy3 in different environments

Cy3, a cyanine dye, is one of the most widely used dyes in investigating the structure and dynamics of biomolecules by means of fluorescence methods. However, Cy3 fluorescence emission is strongly competed by trans-cis isomerization, whose efficiency is dictated by the isomerization energy barrier and the environment of Cy3. The fluorescence quantum yield of Cy3 is very low when the dye is free in homogeneous solution but it is considerably enhanced in an environment that rigidifies the structure, e.g. when it is attached to a DNA strand. In this work, the barriers for isomerization on the excited state of free Cy3, and Cy3 attached to single- and double-stranded DNA in methanol, are presented. The free energy and subsequently the isomerization barrier calculations are performed using the umbrella sampling technique with the weighted histogram analysis method. The hybrid quantum mechanics/molecular mechanics (QM/MM) approach is employed to provide the potential energy surfaces for the excited state dynamics simulations in umbrella sampling. The semiempirical floating occupation molecular orbital configuration interaction method is used for electronic excited state calculations of the QM region (Cy3). From the free energy calculations, the barrier of Cy3 attached to the single-stranded DNA is highest, in agreement with previously reported experimental results. This is likely due to the stacking interaction between Cy3 and DNA. Such a stacking interaction is likely associated with steric hindrance that prevents the rotation around the conjugated bonds of Cy3. If Cy3 experiences high steric hindrance, it has a higher isomerization barrier and thus the efficiency of fluorescence emission increases.

Exploring the Nature of the H2 Bond. 1. Using Spreadsheet Calculations To Examine the Valence Bond and Molecular Orbital Methods

A three-part project for students in physical chemistry, computational chemistry, or independent study is described in which they explore applications of valence bond (VB) and molecular orbital–configuration interaction (MO–CI) treatments of H2. Using a scientific spreadsheet, students construct potential-energy (PE) curves for several states of H2 from the kinetic and potential energies, calculated from closed-form analytical expressions of the ten unique integrals arising from the Born–Oppenheimer Hamiltonian. For this project students use hydrogen 1s basis functions that include a screening parameter. From the calculated PE curves, they find the dissociation energy, De, and equilibrium internuclear distance, Re. In part I students use the Heitler–London (VB) form of the wave function to obtain the PE curves. In part II they optimize the value of the screening parameter to improve the results, and in part III they explore the treatment of H2, using both the simple MO wave function and the application of CI, with and without screening parameter optimization, to obtain the PE curves. Students compare their De and Re results with the experimental values. A set of questions, exercises, and a sample spreadsheet are provided as Supporting Information.

Theoretical studies of absorption cross sections for the C̃ B12-X̃ A11 system of sulfur dioxide and isotope effects

The C (1)B(2)-X (1)A(1) photoexcitation of SO(2) was studied to investigate excited-state dynamics and the effects of the initial vibrational state. Ultraviolet photoabsorption cross sections (sigma's) of seven isotopologues ((32)S (16)O(2), (33)S (16)O(2), (34)S (16)O(2), (36)S (16)O(2), (32)S(16)O(17)O, (32)S(16)O(18)O, (34)S(16)O(18)O) were computed using the wave packet propagation technique based on the three-dimensional potential energy surfaces of the X and C states, which were calculated using the ab initio molecular orbital configuration interaction method. Numerous wave packet simulations were carried out under the adiabatic approximation and used to calculate the sigma's of the seven isotopologues at 298 K; we concluded that the absorption spectrum of SO(2) can be reliably modeled within the adiabatic framework based on the analysis of the time evolution of the wave packet. The calculated sigma's are in reasonable agreement with the recent experiment in the 190-228 nm region, and the isotope shifts of the peaks for (33)S (16)O(2) and (34)S (16)O(2) relative to the corresponding peaks for (32)S (16)O(2) are in good agreement with the observed data. Relative to the sigma of (32)S (16)O(2), isotopic substitution shows a significant increment for those of (34)S (16)O(2) and (36)S (16)O(2) in the 190-228 nm region. This trend is consistent with the observed data.

Ab initio MO–CI based quantum master equation approach: Exciton dynamics of weakly and strongly coupled J-type aggregates

In order to investigate the time evolutions of electron and hole distributions in weakly and strongly coupled H 2 dimer models, we employ a novel dynamic exciton expression derived from the exciton density matrices calculated by the quantum master equation combined with the ab initio molecular orbital (MO)–configuration interaction (CI) method. The oscillation of exciton distribution over the monomers is observed in case of small inter-monomer distance, where the coupled dipole approximation is invalid. The result originates in the covalent character of inter-monomer interaction in the first excited state, i.e., delocalized character of LUMO distribution.

Theoretical Study on Exciton Dynamics in Dendritic Systems: Exciton Recurrence and Migration

The optical functionalities such as exciton recurrence and migration for dendritic systems, e.g., dendrimers, are investigated using the quantum master equation (QME) approach based on the ab initio molecular orbital configuration interaction (MO-CI) method, which can treat both the coherent and incoherent exciton dynamics at the first principle level. Two types of phenylacetylene dendrimers, Cayley-tree dendrimer and nanostar dendrimer with anthracene core, are examined to elucidate the features of excion recurrence and migration motions in relation to their structural dependences. It is found that the nanostar dendrimer exhibits faster exciton migration from the periphery to the core than Cayley-tree dendrimer, which alternatively exhibits exciton recurrence motion among dendron parts in case of small relaxation parameters. Such strong structural dependence of exciton dynamics demonstrates the advantage of dendritic molecular systems for future applications in nano-optical and light-harvesting devices.

A novel dynamic exciton expression based on the ab initio MO CI based quantum master equation approach

We propose a novel dynamic exciton expression based on the quantum master equation approach using the ab initio molecular orbital (MO) singly excited configuration interaction (CI) method developed in our previous paper [M. Nakano, M. Takahata, S. Yamada, R. Kishi, T. Nitta, K. Yamaguchi, J. Chem. Phys. 120 (2004) 2359]. This expression is derived from the partition of polarization density in the configuration basis into the electron and hole contributions, and can describe both the coherent and incoherent dynamics of electron and hole density distributions, e.g., dynamic electric polarization, exciton recurrence and exciton migration.

Analysis of the Ultraviolet Absorption Cross Sections of Six Isotopically Substituted Nitrous Oxide Species Using 3D Wave Packet Propagation

The ultraviolet absorption cross sections of six isotopically substituted nitrous oxide species ( 1 4 N 1 4 N 1 6 O, 1 4 N 1 4 N 1 7 O, 1 4 N 1 4 N 1 8 O, 1 4 N 1 5 N 1 6 O, 1 5 N 1 4 N 1 6 O, and 1 5 N 1 5 N 1 6 O) were computed using the wave packet propagation technique to explore the influence of excited-state dynamics, transition dipole surface, and initial vibrational state. Three-dimensional potential energy surfaces for the electronic states of N 2 O related to the experimentally observed photoabsorption between 170 and 220 nm were calculated using the ab initio molecular orbital configuration interaction method. The transition dipole moment surfaces between these states were also calculated. Numerous wave packet simulations were carried out and used to calculate the temperature-dependent photodissociation cross sections of the six isotopically substituted species. The photolytic isotopic fractionation constants determined using the calculated cross sections are in good agreement with recent experiments. The results show that, in addition to the effect of the changed shape of the ground-state vibrational wave function with isotopic substitution, photodissociation dynamics play a central role in determining isotopic fractionation constants.

Spectroscopic properties of Mg-chlorin, Mg-porphin and chlorophylls a, b, c1, c2, c3 and d studied by semi-empirical and ab initio MO/CI methods

The semi-empirical and ab initio molecular orbital/configuration interaction (MO/CI) methods were used to study spectroscopic properties of chlorophylls a, b, c1, c2, c3 and d and magnesium porphin and magnesium chlorin. Energy minimisation at the PM3 level of all chlorophylls put the magnesium atom away from the centre and above the porphyrin ring and the atomic charges on the nitrogen atoms became positive. At the ab initio HF/6-31G* level of calculation the magnesium is centrally located in the porphyrin plane and the atomic charge on the magnesium atom is positive and that on the surrounding nitrogens negative. Three CI methods used, ZINDO/S CIS (15,15), PM3 CISD (5,5) and ab initio CIS (5,5)/6-31G*, obeyed linear correlation between the experimentally observed and calculated spectroscopic transition energies. The PM3 CISD (5,5) method gave best estimates of Qy, Qx and the Soret transition energies, but predicted oscillator strengths poorly. The ZINDO/S CIS (15,15) method gave best results in the overall simulation of the absorption spectra of chlorophylls, both intensities and wavelengths. The effect of solvent co-ordination on the excited states of chlorophyll a and chlorophyll b was also studied. Calculations predict solvent induced spectroscopic shifts of the Qx and Soret transitions but leave the Qy transition almost unshifted. This is a result of solvent-induced energy level shifts and charge redistribution on the magnesium atom of chlorophylls in the excited states. The results are discussed with reference to spectroscopic properties of chlorophylls in solution, chlorophylls in aggregates and in photosynthetic light-harvesting antenna.

Is acetylene radical anion with a trans–bent form observed in matrix experiment? An ab initio study

Based on extensive ab initio calculations of the hyperfine coupling constants of both hydrogen and carbon nuclei of three C2H−2 anions, it is confirmed that an acetylene radical anion has effectively been produced radiolytically in low temperature alkane matrices and it possesses a trans-bent form. The results are derived from different molecular orbital configuration interaction calculations (CIS, CISD, QCISD and MRD-CI) as well as density functional theory (DFT) employing extended basis sets. Both popular DFT methods (BLYP and B3LYP) show some difficulties in calculating the isotropic coupling constants of the carbon nuclei.

Etude théorique de la dissociation de NO par attachement électronique — courbes de potential ab initio de différents états excités de NO −

Potential curves of the first excited states of NO and NO − were produced using molecular orbital configuration interaction (MO-CI) ab initio methods. Electron attachment dissociations were explained using these curves. The most important dissociation observed, N( 2D) + O-( 2P), seems to involve π states (singlet and triplet) or a 1Δ state. Widths of the resonance states 3σ −, 1Δ and 1σ + were calculated.

Configuration interaction effects on He(I) photoelectron spectra of nucleotide bases: Evidence for valence electron hole-mixing in 1,9-dimethylguanine

Semiempirical HAM/3 molecular orbital configuration interaction (CI) calculations have been employed to interpret the gas-phase He(I) photoelectron (PE) spectrum of 1,9-dimethylguanine (1,9-DMG). Previous interpretation of the PE spectrum of this molecule, which has a tautomeric structure similar to that of guanine in DNA and RNA, has relied on SCF calculations. Test calculations were performed on pyrimidine. Because HAM/3 calculations without CI were parameterized to describe PE data, ionization potentials (IPS) obtained at the SCF level agree better with experiment than IPS obtained with CI calculations. However, when pyrimidine results from the HAM/3 CI calculations are compared to previously reported results obtained using the outer-valence Green function (OVGF) method or the two-particle-hole Tamm–Dabcoff Green function approximation (2ph-TDA) method, the agreement is satisfactory. The average difference between corresponding values for the first four IPS of pyrimidine obtained from HAM/3 CI, OVGF, and the 2ph-TDA calculations is less than 0.5 eV. Furthermore, for the seven lowest-energy cation states of pyrimidine, the three computational methods yield normalized coefficients associated with the dominant Koopmans configurations that have squares that differ by less than 0.14. For 1,9-DMG, the results of HAM/3 CI calculations indicate that five of the seven lowest-energy ionization events, previously assigned to the first-to-third and to the sixth- and seventh-highest occupied orbitals, are well described within the framework of Koopmans theorem. On the other hand, the fourth and fifth ionization events in 1,9-DMG result in cation states in which there is significant hole-mixing of Koopmans configurations associated with removal of electrons from the second- and third-highest occupied π orbitals. © 1992 John Wiley & Sons, Inc.

Valence bond approach exploiting Clifford algebra realization of Rumer–Weyl basis

AbstractA detailed algorithm is described that enables an implementation of a general valence bond (VB) method using the Clifford algebra unitary group approach (CAUGA). In particular, a convenient scheme for the generation and labeling of classical Rumer–Weyl basis (up to a phase) is formulated, and simple rules are given for the evaluation of matrix elements of unitary group generators, and thus of any spin‐independent operator, in this basis. The case of both orthogonal and nonrothogonal atomic orbital bases is considered, so that the proposed algorithm can also be exploited in molecular orbital configuration interaction calculations, if desired, enabling a greater flexibility for N‐electron basis‐set truncation than is possible with the standard Gel'fand–Tsetlin basis. Finally, an exploitation of this formalism for the VB method, based on semiempirical Pariser–Parr–Pople (PPP)‐type Hamiltonian and nonorthogonal overlap‐enhanced atomic orbital basis, and its computer implementation, enabling us to carry out arbitrarily truncated or full VB calculations, is described in detail.

Etude theorique des spectres photoelectronique et ultraviolet de l'anion CN −

Molecular orbital configuration interaction (MOCl) ab initio calculations were carried out in order to reproduce the photoionisation spectrum and the UV spectrum of the CN − anion. The photoionisation spectrum is compared with the one obtained experimentally for NaCN, which is dominated by emission from CN −. The potential curves of the first excited states of CN − were calculated. A 3 Σ + state was found at 6.24 eV above the ground state (at the equilibrium distance) and a 3 π state was found at 3.80 eV above the ground state. The first electronic transition was found to be 3Σ +→ X 1Σ + rather than 3π→ X 1Σ + as supposed until now.

A quantum chemical anaylsis of the time-resolved resonance Raman spectrum of 2,5-dimethyl–2,4-hexadiene in the T1 state

Theoretical calculations are presented on 1,3-butadiene and 2,5-dimethyl–2,4-hexadiene (tetramethyl–butadiene or TMB) in ground and excited triplet states. The T1 potential energy surfaces are calculated from extended self-consistent-field–linear combination of atomic orbits–molecular orbital–configuration interaction (SCF-LCAO-MO-CI) theory. Energy minima and equilibrium geometries are determined in T1. Frequencies and normal modes of vibration are calculated for planar geometries in S0 and T1 and for a geometry in T1 twisted 90° around one of the formal C■C double bonds. Energies of higher triplet levels are computed and oscillator strengths for the transitions from T1 to Tn are determined. The displacements in equilibrium geometries between the T1 and Tn levels corresponding to the strongest T1→Tn transitions are calculated and are used to estimate the intensities of the resonance Raman spectra in T1 under the assumption of a predominant Franck–Condon scattering mechanism. For TMB, the calculated resonance Raman spectra are compared with the experimentally observed one. Satisfactory agreement is found between the calculated and observed spectra. An assignment is obtained for the experimentally observed vibrational modes of TMB in T1. From this analysis, it is concluded that for TMB in T1, the main contribution to the observed resonance Raman spectrum is arising from molecules in the planar form.

Ab Initio Molecular Orbital Configuration Interaction study of nitrogen bis(phosphine)nickel(0): differences in electron correlation effects between .eta.1-end-on and .eta.2-side-on nitrogen coordination modes

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAb Initio Molecular Orbital Configuration Interaction study of nitrogen bis(phosphine)nickel(0): differences in electron correlation effects between .eta.1-end-on and .eta.2-side-on nitrogen coordination modesShigeyoshi Sakaki and Katsutoshi OhkuboCite this: J. Phys. Chem. 1989, 93, 15, 5655–5660Publication Date (Print):July 1, 1989Publication History Published online1 May 2002Published inissue 1 July 1989https://doi.org/10.1021/j100352a006RIGHTS & PERMISSIONSArticle Views69Altmetric-Citations4LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (804 KB) Get e-Alerts

Theoretical study of oxygen atom (1D) insertion into methane.

Ab initio molecular orbital configuration interaction calculations were carried out on the intrinsic reaction coordinate (IRC) path of the reaction CH4+ O (1D) →CH3OH. The oxygen atom (1D) approaches methane along the C3 rotational axis of C3v, symmetry on the lowest potential energy path of the ground state. The ground state and four kinds of excited states of methanol originate from CH4+ O (1D). The reaction system of CH4+ O (1S) generates a higher excited state than those from CH4+ O (1D). It was confirmed that the ground state function along the IRC path can be approximately expressed by the Hartree Fock function near the saddle point. The increase of antibonding δ character with the C-O bond formation is the origin of the elevation of energies and the splitting of the five excited states.

On the primary process in the plasma-chemical and photochemical vapor deposition from silane. III. Mechanism of the radiative species Si*(1P ) formation

The mechanism of the radiative species Si*(1P0) formation from SiH4 was investigated with ab initio molecular orbital–configuration interaction calculations on two reaction routes: (a) the simplest one-step reaction mechanism SiH4→Si+2H2 and (b) the second simplest two-step reaction mechanism SiH4→SiH2+H2→Si+2H2. The conclusions obtained are as follows: (i) the one-step mechanism (a) operates effectively in the generation of the radiative species Si*(1P0), (ii) no effective path was found for the formation of Si*(1P0) in the two-step mechanism, (iii) the radiative species Si*(1P0) originates from the fifth lowest excited singlet state 11T1 of SiH4 at the Td structure in the one-step mechanism (a), whereas the nonradiative species Si(1D) is produced spontaneously from the fourth lowest excited singlet state 11E in both reaction mechanisms of (a) and (b), (iv) the nonradiative species SiH2(11B1) is spontaneously generated from the lowest excited singlet state 11T2 of SiH4, (v) the electronic state of the radiative Si*(1P0) has Rydberg character and the emission of Si*(1P0) at 288.2 nm is approximately expressed by 3p4s(1P0)→3p2(1D) where 4s is a Rydberg atomic orbital (AO). It was also concluded that the contributions of 3d AOs are important for making a description of the quantitative energy separations among the lower lying singlet states, 1D, 1S, and 1P0 of Si atoms.

Excitons in the polyenes

The excited electronic states of an infinite, all-trans, polyene are calculated using a Wannier function expansion. The relationship between these states and the excited electronic states of the finite polyenes, as found in molecular orbital configuration interaction studies, is explored.

Theory of Isotropic Hyperfine Interactions in Pi-Electron Free Radicals. I. Basic Molecular Orbital Theory with Applications to Simple Hydrocarbon Systems

The general molecular orbital configuration interaction approach formulated by McConnell and others is used to express the hyperfine coupling matrix QA in terms of the properties of localized sigma bonds. [QA relates the coupling constant aA, A being 1H or any first row element, to the pi-electron spin-density matrix ϱπ through the expression aA =;trace (ϱπQA).] An important step is the inclusion of all overlap in the basis-set inner- and valence-shell atomic orbitals; failure to do this leads to artificial sensitivity of QA to sigma-bonding details. An orthonormal set of localized sigma-bond orbitals is generated from “equivalent” (two-center) orbitals by a transformation involving various overlap matrices. An approximation to this transformation is used to examine the salient features of QA. The theory supports the first approximation for aA in terms of diagonal elements of QA and ϱπ: aA≈QAAAρAAπ + ΣXQXXAρXXπ, where ρAAπ and ρXXπ are the pi-electron “spin densities” on atom A and its nearest neighbors. Contributions from inner-shell orbitals and interactions between sigma bonds are very important. It is shown that QAAA is particularly insensitive to environmental effects. The adjacent atom parameter QXXA involves contributions from all substituents on A (if any) and on X. If A is a multivalent atom these contributions occur with both positive and negative signs so that the ratio QXXA / QAAA is quite small and can, in principle, be either positive or negative, contrary to previous predictions. Application of the theory to the CH3 radical gives results which agree with experiment to well within the inherent uncertainties in the calculation. The CH3 results are used to choose semiempirical “excitation energies” for a calculation of QC and QH in a hypothetical CH2CH2±ion. For CH2CH2± the large diagonal elements of Q̄C and Q̄H (which include a zero-point “vibrational contribution”) are estimated as (in gauss) : Q̄CCC = +37.8 ± 3.0, Q̄C′C′C = −9.0 ± 1.0 and Q̄CCH = −27.2 ± 1.8. The first and last of these can be compared with the values observed in CH3, +38.3 and −23.0 G, respectively, showing that Q̄CCC is quite insensitive to the substituents on C but that Q̄CCH increases significantly with substitution on C. It is shown that these values of Q̄CCC and Q̄C′C′C give excellent agreement with experimental 13C data on selected aromatic radicals. The smaller elements of Q̄C and Q̄H are estimated (in gauss) : Q̄CC′C = +1.8, Q̄CC′H = −3.0, Q̄C′C′H = +1.8. The estimate of the off-diagonal element QCC′His in good agreement with empirical values which have been obtained for aromatic systems. Using CH3 as a model, the derivatives of QCCH and QCCC with respect to bond length and the effective nuclear charge of carbon are calculated and found to be an order of magnitude smaller than the results obtained by neglecting overlap.

Configuration Interaction in Molecular-Orbital Theory

The importance of configuration interaction within the framework of a Pariser-Parr treatment of π systems is reviewed and further studied. Three molecules—octatetraene, styrene, and naphthalene—are considered in detail. The energies obtained for the various states are shown to be often quite dependent upon the number of configurations included. Finally, it is argued that, if molecular-orbital configuration interaction is to be of predictive value over a wide range of compounds, then the best general criterion for inclusion of a configuration should be its energy, and that the cutoff point should not be less than 20 eV.