QM/MM study of the absorption spectra of DsRed.M1 chromophores

We report geometries and vertical excitation energies for the red and green chromophores of the DsRed.M1 protein in the gas phase and in the solvated protein environment. Geometries are optimized using density functional theory (DFT, B3LYP functional) for the isolated chromophores and combined quantum mechanical/molecular mechanical (QM/MM) methods for the protein (B3LYP/MM). Vertical excitation energies are computed using DFT/MRCI, OM2/MRCI, and TDDFT as QM methods. In the case of the red chromophore, there is a general blue shift in the excitation energies when going from the isolated chromophore to the protein, which is caused both by structural changes and by electrostatic interactions with the environment. For the lowest ππ* transition, these two factors contribute to a similar extent to the overall DFT/MRCI shift of 0.4 eV. An enlargement of the QM region to include active‐site residues does not change the DFT/MRCI excitation energies much. The DFT/MRCI results are closest to experiment for both chromophores. OM2/MRCI and TDDFT overestimate the first vertical excitation energy by 0.3–0.5 and 0.2–0.4 eV, respectively, relative to the experimental or DFT/MRCI values. The experimental gap of 0.35 eV between the lowest ππ* excitation energies of the red (cis‐acylimine) and green (trans‐peptide) forms is well reproduced by DFT/MRCI and TDDFT (0.32 and 0.37 eV, respectively). A histogram spectrum for an equal mixture of the two forms, generated by OM2/MRCI calculations on 450 snapshots along molecular dynamics trajectories, matches the experimental spectrum quite well, with a gap of 0.23 eV and an overall blue shift of about 0.3 eV. DFT/MRCI appears as an attractive choice for calculating excitation energies in fluorescent proteins, without the shortcomings of TDDFT and computationally more affordable than CASSCF‐based approaches. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Predicting absorption spectra of silver-ligand complexes

The detailed structures of most of ligand-stabilized metal nanoclusters (NCs) remain unknown due to the absence of crystal structure data for them. In such a situation, quantum-chemical modeling is of particular interest. We compared the performance of different theoretical methods of geometry optimization and absorption spectra calculation for silver-thiolate complexes. We showed that the absorption spectra calculated with the ADC(2) method were consistent with the spectra obtained with CC2 method. Three DFT functionals (B3LYP, CAM-B3LYP, and M06-2X) failed to reproduce the CC2 absorption spectra of the silver-thiolate complexes.     

Theoretical studies on structures and electronic spectra of linear carbon chains C2nH+ (n = 1−5)

The density functional theory (DFT) and the complete active space self‐consistent‐field (CASSCF) method have been used for full geometry optimization of carbon chains C_2nH⁺ (n = 1–5) in their ground states and selected excited states, respectively. Calculations show that C_2nH⁺ (n = 1–5) have stable linear structures with the ground state of X³Π for C₂H⁺ or X³Σ^? for other species. The excited‐state properties of C_2nH⁺ have been investigated by the multiconfigurational second‐order perturbation theory (CASPT2), and predicted vertical excitation energies show good agreement with the available experimental values. On the basis of our calculations, the unsolved observed bands in previous experiments have been interpreted. CASSCF/CASPT2 calculations also have been used to explore the vertical emission energy of selected low‐lying states in C_2nH⁺ (n = 1–5). Present results indicate that the predicted vertical excitation and emission energies of C_2nH⁺ have similar size dependences, and they gradually decrease as the chain size increases. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Optical Spectra of Oligofurans: A Theoretical Approach to the Transition Energies,Reorganization Energies,and the Vibronic Activity

There is experimental evidence of high vibronic activity that accompanies the allowed transition between the ground state and the lowest electronic singlet excited state of oligofurans that contain two, three, and four furan rings. The absorption and emission spectra of the three lowest oligofurans measured at liquid nitrogen temperature show distinct fine structures that are reproduced using the projection-based model of vibronic coupling (with Dushinsky rotation included) parameterized utilizing either Density Functional Theory (DFT, with several different exchange-correlation functionals) or ab initio (CC2) quantum chemistry calculations. Using as a reference the experimental data concerning the electronic absorption and fluorescence for the eight lowest oligofurans, we first analyzed the performance of the exchange-correlation functionals for the electronic transition energies and the reorganization energies. Subsequently, we used the best functionals alongside with the CC2 method to explore how the reorganization energies are distributed among the totally symmetric vibrations, identify the normal modes that dominate in the fine structures present in the absorption and emission bands, and trace their evolution with the increasing number of rings in the oligofuran series. Confrontation of the simulated spectra with the experiment allows for the verification of the performance of the selected DFT functionals and the CC2 method.     

An exploration of conformational search of leucine molecule and their vibrational spectra in gas phase using ab initio methods

An extensive exploration of the conformational space has been carried out to characterize all possible gas phase structures of leucine. A total of 324 unique trial structures for canonical leucine were generated by considering all possible combinations of single bond rotamers. All trial structures were optimized at the B3LYP/6-311G* level of the DFT method. A total of 77 unique and stationary canonical conformers were found. Further, 15 most stable conformers were reoptimized at B3LYP/6-311++G** level and their respective relative energies, vertical ionization energies, hydrogen bonding patterns, rotational constants and dipole moments were calculated. A single point energy calculations for leucine conformers have also been done at both B3LYP/6-311++G(2df, p) and MP2/6-311++G(2df, p) levels. The good agreement between our estimates of rotational constants for two most stable conformers and available experimental measurements supports the reliability of the B3LYP/6-311++G** level of theory for describing the conformational behavior of leucine molecule. The proton affinity and gas phase basicity were also determined. Using the statistical approach, conformational distributions at various temperatures have also been performed and analyzed. Vibrational spectra were also calculated. It is also observed that zwitterions of leucine are not stable in gas phase.     

Experimental and theoretical electronic absorption spectra of 2,4‐diphenyl‐1,5‐benzothiazepine and its derivatives: Solvatochromic effect and time dependent density functional theory approach

Electronic spectra of 2,4‐diphenyl‐1,5‐benzothiazepine and some of its derivatives in 1,2‐dichloromethane and ethanol are investigated experimentally and theoretically using the time dependent density functional theory (TD‐DFT) method at the B3LYP/6‐311G** level of the theory. The origin of the spectrum of the parent compound is found to be an additive one. The observed ultra violet (UV) spectra in both solvents show two bands S1 in the range between 312–334 nm and S2 in the range between 248–272 nm. The solvent effect is investigated experimentally and theoretically and a blue shift is observed, which is explained in terms of a hydrogen bond model between the solvent and the most negative site of the solute (N atom). This theoretical model is robust in reproducing the experimental blue shift and calculating the hydrogen bond energy and hydrogen bond length. The extent of delocalization and charge transfer processes of the studied compounds is estimated and discussed in terms of natural bond orbital (NBO) analysis and second order perturbation interactions (E²) between donors and acceptors. The effect of substituents of the studied compounds in both solvents shows a noticeable red shift attributed to hyperconjugation effects of the π electron systems of the different moieties.     

Synthesis, molecular structure and vibrational spectra of a dimeric complex formed by cobalt and glycine

The structure of [Co(gly)(2)(OH)(2)].1.5(H(2)O) was solved by X-ray diffraction. It crystallizes in the space group P-1, with two independent dimmers in the unit cell. The results for the calculated vibrational spectra are in good agreement with the experimental one. The infrared spectrum and ab initio calculations are consistent with the crystallographic results.     

Theoretical analysis of excited states and energy transfer mechanism in conjugated dendrimers

The excited states of the phenylene ethynylene dendrimer are investigated comprehensively by various electronic‐structure methods. Several computational methods, including SCS‐ADC(2), TDHF, TDDFT with different functionals (B3LYP, BH&HLYP, CAM‐B3LYP), and DFT/MRCI, are applied in systematic calculations. The theoretical approach based on the one‐electron transition density matrix is used to understand the electronic characters of excited states, particularly the contributions of local excitations and charge‐transfer excitations within all interacting conjugated branches. Furthermore, the potential energy curves of low‐lying electronic states as the functions of ethynylene bonds are constructed at different theoretical levels. This work provides us theoretical insights on the intramolecular excited‐state energy transfer mechanism of the dendrimers at the state‐of‐the‐art electronic‐structure theories. © 2014 Wiley Periodicals, Inc.     

PM3 geometry optimization and CNDO/S-CI computation of UV/Vis spectra of large organic structures: Program description and application to poly(triacetylene) hexamer and taxotere

SIXW.C, a new C version of the computer program CNDUV99 (based on CNDO/S-CI with inclusion of doubly excited configurations) is described and shown to be useful for the computation of the UV/Vis spectra of fairly large molecules. The geometries of the molecules were obtained by our C version of program PM3. To demonstrate the broad applicability of program SIXW.C we have chosen two representative examples: first, a linearly conjugated oligomer of defined length; and, second, a natural product that currently plays a very significant role in cancer therapy. The first molecule is a recently synthesized linearly conjugated monodisperse hexamer of ∼4.6 nm in length (C₁₂₆H₂₂₂O₁₂Si₁₄), with poly(triacetylene) backbone. Despite the 36 conjugated C-atoms of the framework, it exhibits remarkable thermal and environmental stability, which allows in-depth investigation of its physical properties. Therefore, this made it a very attractive candidate for comparison of the theoretically calculated and experimentally measured UV/Vis spectra, as there is still considerable interest in predicting linear optical properties of large conjugated organic molecules at the border to polymers. The agreement between experimental and calculated spectra is better with the UHF-PM3- rather than with the RHF-PM3-optimized structure of the molecule, showing, for the former, excellent agreement between the experimental and theoretical longest wavelength maximum (λ_max), which differ by only 16 nm (802 cm⁻¹). This result is of fundamental interest, because the electronic structure reveals a spin-polarized character, usually referred to as spin density wave. In addition to the flat poly(triacetylene) oligomer, we have calculated N-tert-butoxycarbonyl-10-deacetyl-N-debenzoyltaxol (C₄₃H₅₃NO₁₄, taxotere) as an example for a three-dimensional molecule for which, until now, only MM2 force-field computations were performed. It is closely related to the potent inhibitor of cell division, taxol, which was isolated first in 1971 from the stem bark of the yew Taxus brevifolia Nutt. Taxotere is one of the key weapons in modern cancer therapy. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 396–411, 1999     

Symmetric ring puckering potential in thietane‐1,1‐dioxide compared with experiment and analysis of theoretical vibrational spectra

We studied the ring puckering potential in thietane‐1,1‐dioxide with different methods, using a suitable basis set, 6‐311+G**. We obtained a barrier to ring puckering of 153 cal/mol with the DFT/B3LYP (Becke3 exchange–Lee, Yang, Parr correlation functional) method, ～60% too small compared with experiment. However, using MP2, MP3, and MP4 we obtained values around 200% too large. The MP series turned out to converge far too slowly to the experimental barrier value, showing no sign of convergence even at MP4, while higher orders are out of our reach for such a system. Obviously, of all methods used, DFT worked best despite some shortcomings. The barrier corresponds to 77 K; thus, there should be rapid interconversion over the barrier at room temperature, a phenomenon actually observed at room temperature, the measured barrier corresponding to 201 K. Thus, we decided to use the DFT/6‐311+G** calculations to predict reasonable vibrational spectra and assignments of the lines found. The ring puckering mode is found at 80 cm^?1 in DFT in good agreement with the experimental value of 78.3 cm^?1 for this vibration. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

DFT investigation of sites of protonation of antitumor of 2‐(4‐aminophenyl)benzazoles in the gas phase and in solution

The proton affinity on each of the possible sites in the antitumor 2‐(4‐aminophenyl)benzazoles has been calculated at the B3LYP/6‐311G** level of theory in the gas phase and in solution. The N₃‐site of protonation is found to be strongly favored over the NH₂‐site for the studied compounds both in gas phase and in solution. The stability of N₃‐protonated species is explained by the resonance interaction of the NH₂‐group with the heterocyclic ring. The potential energy surface (PES) for the protonation process was studied at the density functional theory (DFT)/B3LYP/6‐311++G** level of theory. Solvent effects on the PES were also examined using two models: Onsager self‐consistent field and polarizable continuum model (PCM). © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Theoretical study of methoxy group influence in the gas‐phase elimination kinetics of methoxyalkyl chlorides

The unimolecular gas‐phase elimination kinetics of 2‐methoxy‐1‐chloroethane, 3‐methoxy‐1‐chloropropane, and 4‐methoxyl‐1‐chloroburane has been studied by using density functional theory (DFT) methods to propose the most reasonable mechanisms of decomposition of the aforementioned compounds. Calculation results of 2‐methoxy‐1‐chloroethane and 3‐methoxy‐1‐chloropropane suggest dehydrochlorination through a concerted nonsynchronous four‐centered cyclic transition state (TS) to give the corresponding olefin. In the case of 4‐methoxyl‐1‐chloroburane, in addition to the 1,2‐elimination mechanism, the anchimeric assistance by the methoxy group, through a polar five‐centered cyclic TS, provides additional pathways to give 4‐methoxy‐butene, tetrahydrofuran and chloromethane. The bond polarization of the C? Cl, in the direction of C^δ+ ··· Cl^δ?, is the limiting step of these elimination reactions. The significant increase in rate together with the formation of a cyclic product tetrahydrofuran in the gas‐phase elimination of 4‐methoxyl‐1‐chloroburane is attributed to neighboring group participation of the oxygen of the methoxy group in the TS. The theoretical calculations show a good agreement with the reported experimental results. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

A theoretical study of the dihydrogen molecule confined inside carbon nanotubes

The aim of this work is to better understand the interaction between the confined dihydrogen molecule and armchair (2,2), (3,3) (4,4), (5,5), and (6,6) single‐walled carbon nanotubes (SWNT) using Restricted Hartree–Fock (RHF) and Density Functional Theory (DFT) methods using B3LYP and CAM‐B3LYP functionals. Depending on the calculation method and its orientation inside the nanotube, H₂ binds differently. We found that H? H bond length increases when H₂ is trapped in CNT (2,2) and decreases for CNT (3,3) and (4,4). The characteristics of confined H₂ in (5,5) and (6,6) nanotubes are similar to H₂ in a free state. © 2013 Wiley Periodicals, Inc.     

Studies on the Electronic Structures and Spectra of C78（CH2）3

The structures and spectra of 20 possible isomers of C78(CH2)3 have been studied by using AM1,INDO/CIS and DFT methods. The results show that the most stable isomer is 1,2,3,4,5,6-C78(CH2)3 (A) with annulene structures,where three -CH2 groups are added to the 6/6 bonds located at the same hexagon passed by the shortest axis of C78 (C2v). Compared with that of C78 (C2v),the first absorption in the electronic spectrum of C78(CH2)3 (A) is blue-shifted because of its wider LUMO-HOMO energy gap. While the IR frequencies of the C–C bonds on the carbon cage are red-shifted owing to the formation of annulene structures and the extension of the conjugated system. The chemical shifts of the carbon atoms in 13C NMR spectra are moved upfield upon the addition.     

Some theoretical and practical aspects in the separation of humic substances by combined liquid chromatography methods

Permanent need to understand nature, structure and properties of humic substances influences also separation methods that are in a wide scope used for fractionation, characterization and analysis of humic substances (HS). At the first glance techniques based on size-exclusion phenomena are the most useful and utilized for relating elution data to the molecular mass distribution of HS, however, with some limitations and exceptions, respectively, in the structural investigation of HS. The second most abundant separation mechanism is reversed-phase based on weak hydrophobic interactions beneficially combined with the step gradients inducing distinct features in rather featureless analytical signal of HS. Relatively great effort is invested to the developments of immobilized-metal affinity chromatography mimicking chelate-forming properties of HS as ligands in the environment. Surprisingly, relatively less attention is given to the ion-ion interactions based ion-exchange chromatography of HS. Chromatographic separation methods play also an important role in the examination of interactions of HS with pesticides. They allow us to determine binding constants and the other data necessary to predict the mobility of chemical pollutants in the environment. HS is frequently adversely acting in analytical procedures as interfering substance, so more detailed information is desired on manifestation of its numerous properties in analytical procedures. The article topic is covered by the review emphasizing advances in the field done in the period of last 10 years from 2000 till 2010.     

Lipid analysis by thin-layer chromatography--a review of the current state

High-performance thin-layer chromatography (HPTLC) is a widely used, fast and relatively inexpensive method of separating complex mixtures. It is particularly useful for smaller, apolar compounds and offers some advantages over HPLC. This review gives an overview about the special features as well as the problems that have to be considered upon the HPTLC analysis of lipids. The term "lipids" is used here in a broad sense and comprises fatty acids and their derivatives as well as substances related biosynthetically or functionally to these compounds. After a short introduction regarding the stationary phases and the methods how lipids can be visualized on an HPTLC plate, the individual lipid classes will be discussed and the most suitable solvent systems for their separation indicated. The focus will be on lipids that are most abundant in biological systems, i.e. cholesterol and its derivates, glycerides, sphingo- and glycolipids as well as phospholipids. Finally, a nowadays very important topic, the combination between HPTLC and mass spectrometric (MS) detection methods will be discussed. It will be shown that this is a very powerful method to investigate the identities of the HPTLC spots in more detail than by the use of common staining methods. Future aspects of HPTLC in the lipid field will be also discussed.