Charge-transfer transitions in protein circular dichroism calculations

Charge-transfer transitions in proteins play a key role in many biophysical processes, from the behavior of redox proteins to photochemical reactions. We present ab initio calculations on a model dipeptide and more approximate calculations of the electronic excited states of proteins which, taken together, provide the most definitive assignment and characterization of charge-transfer transitions in proteins to date. We have calculated from first principles the electronic circular dichroism (CD) spectra of 31 proteins on the basis of their structures. Compared to previous studies, we achieve more accurate calculated CD spectra between 170 and 190 nm, owing mainly to the importance in alpha-helices of a charge-transfer transition from the lone pair on one peptide group to the pi* orbital on the next peptide group.     

Tailoring transition metal complexes for nonlinear optics applications. 2. A theoretical investigation of the second-order nonlinear optical properties of M(CO)(5)L complexes (M = Cr, W; L = Py, PyCHO, Pyz, PyzBF(3), BPE, BPEBF(3))

In this work, we report an ab initio investigation of second-order nonlinear optical (NLO) properties and absorption electronic spectra of push-pull transition metal chromophores of the formula [M(CO)(5)L] (M = Cr, W; L = pyridine (Py), 4-formyl-pyridine (PyCHO), pyrazine (Pyz), trans-1,2-bis(4-pyridyl)ethylene (BPE)). Pyz and BPE are considered either with one nitrogen atom free or interacting with the strong acceptor BF(3). All of the molecular properties have been calculated using two different and methodologically independent approaches: the time dependent and coupled perturbed density functional theories (TDDFT and CPDFT) and the sum-over-states (SOS) approach, where the excited states are obtained via the single configuration interaction (SCI) ab initio method. DFT results are in acceptable agreement with the experimental energy values of electronic transitions (with the exception of chromophores with the large pi-delocalization, like BPE); SCI calculations overestimate excitation energies and produce an inversion in the order of d(M) --> pi(L) and d(M) --> pi(CO) transitions. The SCI-SOS approach gives first-order hyperpolarizabilities, basically in agreement as trend and values with the experiments and seems to be a tool generally suitable for the evaluation of these properties also for transition metal complexes. On the other hand, the first-order hyperpolarizabilities computed using the CPDFT approach are consistently overestimated in comparison with the experimental results, especially in the case of a ligand with large pi-delocalization. We also show that the "two-level" approximation taking into account only the lowest energy charge transfer excitation (e.g., d(M) --> pi(L)) is not applicable to chromophores with the extended pi-delocalized ligand (BPE) coordinated to a transition metal, due to significant contributions originating from intraligand pi(L) --> pi(L) transitions. This study reports a detailed analysis and comparison of electronic NLO effects of transition metal complexes computed with DFT and ab initio SCI-SOS methodology.     

The interplay of thio(seleno)amide/vinylogous thio(seleno)amide "resonance" and the anisotropic effect of thiocarbonyl and selenocarbonyl functional groups

Amino-substituted thio(seleno)acrylamides 1-4 were synthesized and their 1H and 13C NMR spectra assigned. Both the NMR data and the results of theoretical calculations at the ab initio level of theory were employed to elucidate the adopted structures of the compounds in terms of E/Z isomerism and s-cis/s-trans configuration. In the case of the asymmetrically N(Me)Ph-substituted compounds, ab initio GIAO-calculated ring current effects of the N-phenyl group were applied to successfully determine the preferred conformer bias. The restricted rotations about the two C-N partial double bonds were studied by DNMR and the barriers to rotation (DeltaG(c)++) determined at the coalescence temperatures, and these were discussed with respect to the structural differences between the compounds. The barriers to rotation were also calculated at the ab initio level of theory where the best results (R(2) = 0.8746) were obtained only with inclusion of the solvent at the SCIPCM-HF/6-31G* level of theory. The calculations also provided means of assessing structural influences which were not available due to inaccessible rotation barriers. By means of natural bond orbital (NBO) analysis of 1-4, the occupation numbers of nitrogen lone pairs and bonding/antibonding pi/pi orbitals were shown to quantitatively describe thio(seleno)amide/vinylogous thio(seleno)amide "resonance". Finally, the thio(seleno)carbonyl anisotropic effect was quantitatively calculated by the GIAO method and visualized by isochemical shielding surfaces (ICSS). Only marginal differences between the two anisotropic effects were calculated and are therefore of questionable utility for previous and future applications with respect to stereochemical assignments.     

ⅤA族元素甲基化合物的赝势从头算研究

使用相对论赝势从头算方法研究了XMe3(X=N, P, As, Sb, Bi)系列分子的Koopmans电离能, 孤对电子轨道特征及电子结构, 并将某些分子轨道能与相应X的原子轨道能进行了线性关联。     

Collision-energy-resolved Penning ionization electron spectroscopy of thiazole and benzothiazole: study of ionic states and anisotropic interactions between a metastable He(23S) atom and hetero cyclic compounds

Anisotropic interactions between a metastable He(2(3)S) atom and aromatic heterocyclic compounds (thiazole and benzothiazole) as well as their electronic structures were studied by means of collision-energy/electron-energy resolved two-dimensional Penning ionization electron spectroscopy combined with ab initio molecular orbital calculations. Different collision-energy dependence of partial ionization cross sections (CEDPICS) were clearly observed for different ionic states depending on anisotropic extents of molecular orbitals from which an electron is removed. It was found that thiazole and benzothiazole most strongly attract a He(2(3)S) atom around the region where the nitrogen lone pair orbital extends. For another heteroatom, sulfur, it is relatively weak, but a certain attractive interaction was found for the directions perpendicular to the molecular plane. Benzothiazole was shown to widely attract a He(2(3)S) atom in the out-of-plane directions, since the benzene moiety showed a deeper potential well than the five-membered ring. Assignments of the ionic states including shake-up states were also discussed from observed CEDPICS and ab initio molecular orbital calculations. In particular, for the satellite bands, a negative collision energy dependence of the band intensity was well supported by a configuration-interaction calculation that assigns the satellite bands to be the ionization from pi orbitals accompanying pi-pi or n-pi excitations.     

pi Molecular Orbital Crossing a(2)(chi)/b(1)(psi) in 1,10-Phenanthroline Derivatives. Ab Initio Calculations and EPR/ENDOR Studies of the 4,7-Diaza-1,10-phenanthroline Radical Anion and Its M(CO)(4) Complexes (M = Cr, Mo, W)

Ab initio, semiempirical, and HMO perturbation calculations were employed to assess the relative positioning of the closely situated low-lying unoccupied pi MOs a(2)(chi) and b(1)(psi) in 1,10-phenanthroline (phen) and its 3,4,7,8-tetramethyl (tmphen) and four symmetrical diaza derivatives (n,m-dap). Compared to a(2)(chi), the b(1)(psi) pi MO is distinguished by markedly higher MO coefficients at the chelating nitrogen pi centers in 1,10-positions; eventually, a higher Coulomb integral value at those positions will thus always favor the lowering of b(1) beyond a(2). Using the Coulomb integral parameter at the chelating 1,10-nitrogen pi centers as the HMO perturbation variable, the crossing of both energy levels in terms of decreasing preference for the a(2)(chi) over the b(1)(psi) orbital as the lowest unoccupied MO follows the sequence 5,6-dap > 2,9-dap > 4,7-dap > phen > 3,8-dap. The calculations reveal a(2)(chi) as the LUMO in 5,6-dap for all reasonable perturbation parameters, in agreement with previous observations for ruthenium(II) complexes which reveal a discrepancy between the lowest-lying "redox pi orbital" (a(2)) and the "optical pi MO" (b(1)) to which the most intense low-energy MLCT transition occurs. According to the HMO calculations, the situation is more ambiguous for the 4,7-dap analogue, yet EPR/ENDOR studies clearly show that the one-electron-reduced ligand and its tetracarbonylmetal(0) complexes (Cr, Mo, W) have the b(1)(psi) orbital singly occupied. Only ab initio calculations with double-zeta basis and inclusion of d polarization functions reproduced correctly the experimentally observed orbital ordering for tmphen (a(2) < b(1)) and for phen and 4,7-dap (b(1) < a(2)).     

Electronic structure and ionization energies of palladium and platinum N-heterocyclic carbene complexes

Density functional methods have been used to calculate the geometries, electronic structure and ionization energies (IE) of N-heterocyclic carbene complexes of palladium and platinum, [M(CN2R2C2H2)2](M = Pd, Pt; R = H, Me, Bu t). Agreement with X-ray structures (R = Bu t) was good. Calculated IE agreed well with the photoelectron (PE) spectra (R = Bu t); metal bands were calculated to be within 0.25 eV of the experimental values, whereas the higher lying ligand bands deviated by up to 0.9 eV. Spin-orbit methods were needed to achieve this level of agreement for the Pt complex, but the calculations were found to underestimate the spin-orbit splitting somewhat. The principal metal-ligand bonding is between the carbene lone pair HOMO and a (d(z2)+ s) hybrid on the metal. The metal p(z) orbital contributes very little to the bonding. The metal d(xz,yz) orbitals mix primarily with the filled pi3 orbitals on the ligands and secondarily with the empty pi5 orbitals. Consequently they are little stabilized in comparison to the metal d(xy,x2- y2) orbitals, which are non-bonding in the complex. The first PE band for both the Pd and Pt complexes is from ionization of a (s - d(z2)) hybrid orbital. The IE is greater for Pt than for Pd on account of the post-lanthanide relativistic stabilization of the Pt 6s orbital.     

Theoretical and spectroscopic study of nickel(II) porphyrin derivatives

A set of substituted (sulfonate, amino) nickel porphyrin derivatives such as phthalocyanine and phenylporphyrin was studied by spectroscopic (UV-vis, FTIR, XPS) and quantum-chemical methods. The Q and Soret bands were identified in the UV-vis spectra of aquo solutions of the tetrasulfo-substituted complexes and in DMF and ACN solutions of the amino-substituted phenylporphyrin and phthalocyanine Ni(II) complexes, respectively. In all the complexes the frontier molecular orbitals predict that the oxidation and reduction sites are localized on the ligand rather than in the metal atom. A natural bonding orbital (NBO) analysis of all the complexes showed that a two-center bond NBO between the pyrrolic nitrogens (Npyrr) and the nickel atom does not exist, the Npyrr...Ni interaction occurring instead by a delocalization from one lone pair of each Npyrr toward one lone pair of the nickel atom, as estimated by second-order perturbation theory. The calculated values of electronic transitions between the frontier molecular orbitals are in good agreeement with the UV-vis data. At the theoretical level, we found that while the ligand effect is more important in the Q-band (approximately 16 kcal/mol), the substituent effect is more significant in the Soret band (approximately 9 kcal/mol). A good agreement was also found between the experimental and calculated infrared spectra, which allowed the assignment of many experimental bands. The XPS results indicate that the Ni(II) present in the phenylporphyrin structure is not affected by a change of the substituent (sulfonate or amino).     

ZINDO calculations of the ground state and electronic transitions in the tetracyanonickelate Ion,Ni(CN)(4)(2-)

ZINDO semiempirical calculations on the Ni(CN)(4)(2-) ion were performed, and ground-state energies for all 41 valence-orbital-based MOs and orbital transition components of the two lowest energy fully allowed electronic transitions are reported. Gaussian 94 was used to calculate ground-state energies as a comparison. The ground-state energies using ZINDO compare much more favorably with those found through ab initio techniques than with those from a reported INDO calculation. The found electronic transitions agree substantially with earlier assignments with the exception that several orbital transitions are required to adequately model the lowest energy allowed x,y-polarized experimental transition. Calculation parameters were optimized to give excellent agreement with experiment and may serve well for more complex arrangements of this ion.     

Vacuum ultraviolet spectra of CClF2CH2Cl and CClF2CHCl2, and Rydberg assignment based on ab initio molecular orbital calculations

The absorption spectra of CClF₂CH₂Cl and CClF₂CHCl₂ are measured in the spectral range 115–200 nm. The bands observed are assigned on the basis of ab initio molecular orbital calculations. The strong absorption bands in the 115–150 nm range are assigned to the transitions from lone pair orbitals of chlorine atoms to the Rydberg states. The population of the electrons in each molecular orbital (MO) is calculated to clarify the MO character. The four highest MOs for CClF₂CH₂Cl and six for CClF₂CHCl₂, which contribute to the absorption spectra in the 115–150 nm range, are typical chlorine lone pair orbitals, and are responsible for the spectra in this range.     

Ligand to ligand charge transfer in (hydrotris(pyrazolyl)borato)(triphenylarsine)copper(I)

Emission and UV-vis absorption spectra of (hydrotris(pyrazolyl)borato)(triphenylarsine)copper(I), (CuTpAsPh3), (hydrotris(pyrazolyl)borato)(triethylamine)copper(I), (CuTpNEt3), and (hydrotris(pyrazolyl)borato)(triphenylphosphine)copper(I), (CuTpPPh3), are reported. The spectra of the arsine complex contain low-energy bands (with a band maximum at 16,500 cm(-1) in emission and a weak shoulder centered at about 25,000 cm(-1) in absorption) that are not present in the corresponding spectra of the amine or phosphine complexes. The lowest energy electronic transition is assigned to ligand to ligand charge transfer (LLCT) with some contribution from the metal. This assignment is consistent with PM3(tm) molecular orbital calculations that show the HOMO to consist primarily of pi orbitals on the Tp ligand (with some metal orbital character) and the LUMO to be primarily antibonding orbitals on the AsPh3 ligand (also with some metal orbital character). The absorption shoulder shows a strong negative solvatochromism, indicative of a reversal or rotation of electric dipole upon excitation, and consistent with a LLCT. The trends in the energies of the electronic transitions and the role of the metal on the LLCT are discussed.     

Nitrile and thiocyanate IR probes: quantum chemistry calculation studies and multivariate least-square fitting analysis

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

Interpretation of the photoelectron spectra of FeS(2)(-) by a multiconfiguration computational approach

The ground states of FeS(2) and FeS(2)(-), and several low-lying excited electronic states of FeS(2) that are responsible for the FeS(2)(-) photoelectron spectrum, are calculated. At the B3LYP level an open, quasi-linear [SFeS](-) conformation is found as the most stable structure, which is confirmed at the ab initio CASPT2 computational level. Both the neutral and the anionic unsaturated complexes possess high-spin electronic ground states. For the first time a complete assignment of the photoelectron spectrum of FeS(2)(-) is proposed. The lowest energy band in this spectrum is ascribed to an electron detachment from the two highest-lying 3dpi antibonding orbitals (with respect to the iron-sulfur bonding) of iron. The next-lowest experimental band corresponds to an electron removal from nonbonding, nearly pure sulfur orbitals. The two highest bands in the spectra are assigned as electron detachments from pi and sigma bonding mainly sulfur orbitals.     

Very-low-lying electronic states result from n --> pi excitations in open-shell annulenes, annelated with alpha-dicarbonyl groups

UB3LYP/6-31G* calculations find that alpha-dicarbonyl-annelated cyclopentadienyl radical 1 has a sigma ground state, which is formed by excitation of an electron from the in-phase combination of carbonyl lone-pair orbitals into the singly occupied pi orbital. Similarly, tetrakis-annelated cyclooctatetraene 3 is calculated to have very-low-lying singlet and triplet excited states, which result from excitations of electrons from the b1g combination of lone pair orbitals into the empty pi nonbonding MO of the COT ring.     

An Ab initio study of the ligand field and charge-transfer transitions of Cr(CN)(6)(3-) and Mo(CN)(6)(3-)

High-level ab initio calculations on the excited states of Cr(CN)63- and Mo(CN)63- are reported. For the latter complex, a rather large 10 Dq value of 42 000 cm-1 is obtained, reflecting the increased covalency. The lowest lying charge-transfer transitions for both complexes are predicted to be of the type ligand-to-metal, an assignment in agreement with the photochemical behavior of Cr(CN)63-. A good correspondence between the well-known experimental spectrum of the chromium complex and the theoretical CASPT2 excitation energies is found.     

Comparative photophysical properties of free-base, bis-Zn(II), bis-Cu(II), and bis-Co(II) doubly N-confused hexaphyrins(1.1.1.1.1.1)

We have comparatively investigated the photophysics of a series of bis-metal doubly N-confused hexaphyrins(1.1.1.1.1.1) using time-resolved fluorescence, femtosecond transient absorption, two-photon absorption measurements, and geometry-optimized ab initio calculations. Bis-Zn(II) and free-base doubly N-confused hexaphyrins exhibit well-resolved and red-shifted B- and Q-like absorption bands compared with porphyrins. Their allowed transitions are (pi,pi) transitions of the hexaphyrin ring, as confirmed by the HOMO and LUMO frontier orbitals based on ab initio calculations at the B3LYP/6-31G level. On the other hand, the absorption spectra of bis-Cu(II) and bis-Co(II) doubly N-confused hexaphyrins are relatively broad, presumably due to large couplings between the metal d-orbitals and pi-electrons of the hexaphyrin ring. Owing to these couplings, bis-Cu(II) and bis-Co(II) doubly N-confused hexaphyrins have much shorter excited-state lifetimes of 9.4 +/- 0.3 ps and 670 fs, respectively, than those (267 +/- 16 and 62.4 +/- 1.2 ps, respectively) of bis-Zn(II) and free-base doubly N-confused hexaphyrins. The two-photon absorption cross section (sigma(2)) values, which are believed to depend strongly on the ring planarity (pi-conjugation), are in line with the excited-state lifetime trends.     

Lead-poisoned zinc fingers: quantum mechanical exploration of structure, coordination, and electronic excitations

Density functional theory (DFT) structure calculations and time-dependent DFT electronic excitation calculations on simple mononuclear lead structures confirm recent reports on the stabilization of tricoordinated structural domains in poisoned proteins. However, the possibility of the formation of tetracoordinated lead complexes should not be disregarded in studies on mechanisms of lead toxicity because structures with both coordination modes are plausible and might contribute to observed UV spectra. Reported calculations along with detailed molecular orbital analysis confirm that the intense UV signal at around 260 nm is an indicator of the ligand-to-metal charge transfer (LMCT) band where the electrons are transferred from the sulfur 3p orbital to the lead 6p orbital. The composition of the LMCT band reveals significant excitations not only from the Pb-S bonding orbitals but also from sulfur lone-pair orbitals to the Pb-S antibonding orbitals for which the electron density is largely localized on the Pb "6p-like" molecular orbitals. There is a solid indication that the stereochemically active pair orbital of lead is not strongly hybridized and remains largely of the 6s character in tricoordinated lead structures and is minimally hybridized in tetracoordinated lead structures. Computed UV spectra of lead model complexes are compared to experimental UV spectra of model lead peptides. The comparison shows a good agreement with the major spectral trends and changes observed in these experiments.     

Electronic structure of the [MNH2]+ (M = Sc-Cu) complexes

B3LYP geometry optimizations for the [MNH2]+ complexes of the first-row transition metal cations (Sc+-Cu+) were performed. Without any exception the ground states of these unsaturated amide complexes were calculated to possess planar geometries. CASPT2 binding energies that were corrected for zero-point energies and including relativistic effects show a qualitative trend across the series that closely resembles the experimental observations. The electronic structures for the complexes of the early and middle transition metal cations (Sc+-Co+) differ from the electronic structures derived for the complexes of the late transition metal cations (Ni+ and Cu+). For the former complexes the relative higher position of the 3d orbitals above the singly occupied 2p(pi) HOMO of the uncoordinated NH2 induces an electron transfer from the 3d shell to 2p(pi). The stabilization of the 3d orbitals from the left to the right along the first-row transition metal series causes these orbitals to become situated below the HOMO of the NH2 ligand for Ni+ and Cu+, preventing a transfer from occurring in the [MNH2]+ complexes of these metal cations. Analysis of the low-lying states of the amide complexes revealed a rather unique characteristic of their electronic structures that was found across the entire series. Rather exceptionally for the whole of chemistry, pi-type interactions were calculated to be stronger than the corresponding sigma-type interactions. The origin of this extraordinary behavior can be ascribed to the low-lying sp2 lone pair orbital of the NH2 ligand with respect to the 3d level.     

Low energy electron energy-loss spectroscopy of CF3X (X=Cl,Br)

We report threshold electron energy-loss spectra for the fluorohalomethanes CF3X (X=Cl,Br). Measurements were made at incident electron energies of 30 and 100 eV in energy-loss range of 4-14 eV, and at scattering angles of 4 degrees and 15 degrees. Several new electronic transitions are observed which are ascribable to excitation of low-lying states as well as are intrinsically overlapped in the molecules themselves. Assignments of these electronic transitions are suggested. These assignments are based on present spectroscopic and cross-section measurements, high-energy scattering spectra, and ab initio molecular orbital calculations. The calculated potential curves along the C-X bond show repulsive nature, suggesting that these transitions may lead to dissociation of the C-X bond. The present results are also compared with the previous ones for CF3H, CF4, and CF3I.