A theoretical approach to the influence of the macrocycle conformation on the molecular electronic structure in Mg-porphyrins

Nonplanar saddled (sad) ruffled (ruf) and domed (dom) conformations of the Mg-porphyrin (MgP) macrocycle in several degrees of deformation have been computed. These symmetrical distortion modes were induced in unsubstituted macrocycle using molecular definitions for calculations which permits us to achieve a systematical variation of the nonplanarity varying only a convenient geometrical parameter of the molecule. Series of nonplanar macrocycles like those synthesized in previous works employing peripheral substitutions are obtained. The procedure here used to induce deformations gives the possibility of investigating the modulator role of the out-of-plane distortions on the geometry and electronic properties of the porphyrin avoiding additional influences due to the substituents or the surrounding protein scaffolding.     

A Phytochrome Sensory Domain Permits Receptor Activation by Red Light

Optogenetics and photopharmacology enable the spatio‐temporal control of cell and animal behavior by light. Although red light offers deep‐tissue penetration and minimal phototoxicity, very few red‐light‐sensitive optogenetic methods are currently available. We have now developed a red‐light‐induced homodimerization domain. We first showed that an optimized sensory domain of the cyanobacterial phytochrome 1 can be expressed robustly and without cytotoxicity in human cells. We then applied this domain to induce the dimerization of two receptor tyrosine kinases—the fibroblast growth factor receptor 1 and the neurotrophin receptor trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway non‐invasively in mammalian tissue and in multicolor cell‐signaling experiments. The light‐controlled dimerizer and red‐light‐activated receptor tyrosine kinases will prove useful to regulate a variety of cellular processes with light.     

VESPA: A new,fast approach to electrostatic potential-derived atomic charges from semiempirical methods

An improved semiempirical method for computing electrostatic potential-derived atomic charges is described. It includes a very fast algorithm for the generation of the grid points around the molecule and the calculation of the electrostatic potential at these points. The dependency of the atomic point charges obtained on the number of grid points used in the fitting procedure is examined. For “buried” atoms a high density grid is necessary. It is possible to obtain 6–31G*-quality atom-centered point charges, even for phosphorus compounds, using AM1 or PM3. This approach can therefore be recommended for general use in QSAR or molecular mechanics for any organic and bioorganic system up to about 200 atoms. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 744–756, 1997     

Essential amino acids interacting with flavonoids: A theoretical approach

The interaction of two flavonoid species (resorcinolic and fluoroglucinolic) with the 20 essential amino acids was studied by the multiple minima hypersurface (MMH) procedures, through the AM1 and PM3 semiempirical methods. Remarkable thermodynamic data related to the properties of the molecular association of these compounds were obtained, which will be of great utility for future investigations concerning the interaction of flavonoids with proteins. These results are compared with experimental and classical force field results reported in the available literature, and new evidences and criteria are shown. The hydrophilic amino acids demonstrated high affinity in the interaction with flavonoid molecules; the complexes with lysine are especially extremely stable. An affinity order for the interaction of both flavonoid species with the essential amino acids is suggested. Our theoretical results are compared with experimental evidence on flavonoid interactions with proteins of biomedical interest. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Long-Distance Protonation-Conformation Coupling in Phytochrome Species

Phytochromes are biological red/far-red light sensors found in many organisms. The connection between photoconversion and the cellular output signal involves light-mediated global structural changes in the interaction between the photosensory module (PAS-GAF-PHY, PGP) and the C-terminal transmitter (output) module. We recently showed a direct correlation of chromophore deprotonation with pH-dependent conformational changes in the various domains of the prototypical phytochrome Cph1 PGP. These results suggested that the transient phycocyanobilin (PCB) chromophore deprotonation is closely associated with a higher protein mobility both in proximal and distal protein sites, implying a causal relationship that might be important for the global large-scale protein rearrangements. Here, we investigate the prototypical biliverdin (BV)-binding phytochrome Agp1. The structural changes at various positions in Agp1 PGP were investigated as a function of pH using picosecond time-resolved fluorescence anisotropy and site-directed fluorescence labeling of cysteine variants of Agp1 PGP. We show that the direct correlation of chromophore deprotonation with pH-dependent conformational changes does not occur in Agp1. Together with the absence of long-range effects between the PHY domain and chromophore pK_a, in contrast to the findings in Cph1, our results imply phytochrome species-specific correlations between transient chromophore deprotonation and intramolecular signal transduction.     

Electronic spectra and electron structure of fullerene complex (η2-C60)Fe(CO)4

The electronic spectrum of the C₆₀Fe(CO)₄ complex was studied in a toluene solution. The more intense absorption of C₆₀Fe(CO)₄ in the visible region, relative to the free C₆₀, can be attributed to the effect of lower symmetry of the C₆₀ fullerene cage in C₆₀Fe(CO)₄ and, thus, relaxation of selection rules for forbidden internal electronic transitions of C₆₀. No bands of the charge transfer from 3d(Fe) to C₆₀ orbitals were observed in the visible region of the complex spectrum. Assignment of the bands was confirmed by semiempirical calculations of the electronic spectrum.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1453–1458, June, 1996     

A quantum mechanical approach to electrochemical behavior of spirochromics

Fully optimized semiempirical quantum‐chemical calculations of photochromic spiropyrans are presented. The vertical ionization potentials are calculated and their variation with substitutions are correlated to experimental oxidation potentials. The effects of the substitutions are studied and the partial charges on indoline and pyran components generated by HOMO are found to be responsible for the variations. The deactivating groups on the indoline ring system and deactivating groups on the pyran system increase the ionization potential and, consecutively, the oxidation potential. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 75: 111–117, 1999     

From crystal to micelle: A new approach to the micellar structure

The structure of sodium and rubidium deoxycholate micellar aggregates in aqueous solutions was found to be helical and to be stabilized mainly by polar interactions. Astonishingly, the lateral surface of the helix is covered by nonpolar groups and the interior part is filled with cations surrounded by water molecules, as in the case of an inverted micelle. This helical model was inferred from the crystal structures of sodium and rubidium deoxycholates and proved by spectroscopic and diffractometric experimental data. The strategy of the approach to the determination of the micellar structure and the comparison with another model, previously proposed for the bile salt micelles, are reported. On the basis of some results obtained for sodium tauro- and glyco-deoxycholates, micellar models are suggested which could account for the biological function of these important conjugated bile salts.     

Ab initio prediction of vibrational spectra: A database approach

Efforts to develop a database of quadratic force fields for organic molecules are described. The database is based on systematic ab initio calculations, scaled to reproduce the experimentally observed frequencies. The choice of the theoretical method, the basis sets, geometries, internal coordinates and the scaling procedure are discussed. A key point in the procedure is the automatic generation of the internal valence coordinates. This is also very advantageous for geometry optimization. The database should permit the prediction of vibrational frequencies for most organic molecules to 10–20 cm⁻¹, together with semiquantitative intensities. The accuracy is sufficient to identify unknown compounds from a list of reasonable candidates.     

Investigation of UV spectra of isomeric nitropyrazoles by the semiempirical AM1 (CI) method

The absorption bands in the UV spectra of isomeric nitropyrazoles were assigned by the calculations in the semiempirical AMI (CI) approximation. The long-wave absorption of nitropyrazoles is caused by π→π* and η₀→π* transitions. The charge-transfer band is the most intense. The π→π* transitions undergo a considerable bathochromic shift in the deprotonation. The first ionization potential (PI) of the 4-nitropyrazole anion was estimated from the empirical dependence of the energy of the excited π-state on PI of alkyl-substituted 4-nitropyrazoles. The PI of the 4-nitropyrazole anion is 3 eV lower than that of a neutral molecule. This is evidence for a substantial destabilization of the boundary β-orbital in the heterolytic cleavage of the N−H bond. The analysis of the UV and NMR spectra of 3(5)-nitropyrazole confirms the viewpoint that the 3-nitro tautomer predominates in solution. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya. No. 2, pp. 310–314, February, 1997.     

AM1 study of photoelectron spectra

A correlation was found between the group dipole moments of substituents determined from the dipole moments of ethylene derivatives and the second ionization potentials of allene derivatives corresponding to the -MO of the C()-C() bond. It was shown that the concept of the effect of the substituent field cannot completely explain the observed phenomena, and the energies of the second ionic states of bromoallene and alkoxyallenes are lowered because of the interaction between nonbonded fragments through the systems of the compounds. It has been found that, in terms of orbital approximation, this interaction causes electronic destabilization of theanti-planar (trans) conformers of methoxyallene and methyl vinyl ether compared to theirsin-planar (cis) forms.For Part 5, see Ref. 1.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 48–54, January, 1995.     

A semiempirical approach to the intra-phycocyanin and inter-phycocyanin fluorescence resonance energy-transfer pathways in phycobilisomes

A semiempirical methodology to model the intra-phycocyanin and inter-phycocyanin fluorescence resonance energy-transfer (FRET) pathways in the rods of the phycobilisomes (PBSs) from Fremyella diplosiphon is presented. Using the F?rster formulation of FRET and combining experimental data and PM3 calculation of the dipole moments of the aromatic portions of the chromophores, transfer constants between pairs of chromophores in the phycocyanin (PC) structure were obtained. Protein docking of two PC hexamers was used to predict the optimal distance and axial rotation angle for the staked PCs in the PBSs' rods. Using the distance obtained by the docking process, transfer constants between pairs of chromophores belonging to different PC hexamers were calculated as a function of the angle of rotation. We show that six preferential FRET pathways within the PC hexameric ring and 15 pathways between hexamers exist, with transfer constants consistent with experimental results. Protein docking predicted the quaternary structure for PCs in rods with inter-phycocyanin distance of 55.6 A and rotation angle of 20.5 degrees . The inter-phycocyanin FRET constant between chromophores at positions beta(155) is maximized at the rotation angle predicted by docking revealing the crucial role of this specific inter-phycocyanin channel in defining the complete set of FRET pathways in the system.     

Non‐Bonded Interactions Drive the Sub‐Picosecond Bilin Photoisomerization in the Pfr State of Phytochrome Cph1

Phytochromes are protein‐based photoreceptors harboring a bilin‐based photoswitch in the active site. The timescale of photosignaling via C₁₅=C₁₆ E‐to‐Z photoisomerization has been ambiguous in the far‐red‐absorbing P_fr state. Here we present a unified view of the structural events in phytochrome Cph1 post excitation with femtosecond precision, obtained via stimulated Raman and polarization‐resolved transient IR spectroscopy. We demonstrate that photoproduct formation occurs within 700 fs, determined by a two‐step partitioning process initiated by a planarization on the electronic excited state with a 300 fs time scale. The ultrafast isomerization timescale for P_fr‐to‐P_r conversion highlights the active role of the nonbonding methyl–methyl clash initiating the reaction in the excited state. We envision that our results will motivate the synthesis of new artificial photoswitches with precisely tuned non‐bonded interactions for ultrafast response.     

HOUDINI: a new approach to computer-based structure generation

A new method of structure generation called convergent structure generation has been developed to address limitations of earlier methods. The features of the program (HOUDINI) based on this method include the following: a single integrated representation of the collective substructural information; the use of parallel atom groups for efficient processing of families of alternative substructural inferences; and a managed structure generation procedure designed to build required structural features early in the process.     

A new molecular-dynamics based approach for molecular crystal structure search

A new molecular-dynamics based approach is proposed to search for candidate crystal structures of molecular solids. The procedure is based on the observation of spontaneous transitions between ordered and disordered states in molecular-dynamics simulations of an artificial periodic system with a small unit cell. In such a way only the most stable structures are automatically selected. The method can be applied to the solution of crystal structures from low-quality or very complex diffraction data. Tests are presented for H2O-ice polymorphs.     

Synthesis and spectroscopic properties of new water-soluble phthalocyanines containing pyridinium hydrochloride fragments

New 2,9,16,23-tetra[o-(hydroxymethyl)benzyloxy]-substituted phthalocyanines were synthesized. Their reaction with 4-bromopyridine afforded 2,9,16,23-tetra[o-(4-pyridyloxymethyl)benzyloxy]-substituted analogs, treatment of which with HCl led to water-soluble pyridinium salts. Spectroscopic properties of the phthalocyanines obtained were studied and a hypsochromic shift of the Q-band of the hydrochloride as compared with the corresponding pyridinium analogs was observed. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 12, pp. 2350–2354, December, 2007.     

Calculation of molecular vibrations: Selective scaling factors for semiempirical force constants

The complete force constant matrices of a set of 50 aliphatic and aromatic hydrocarbons are calculated at the density functional theory B3LYP/6–31+G(d, p) and semiempirical PM3 levels of theory. After transformation from Cartesian to nonredundant internal coordinates, the errors in the semiempirical force constants are systematically analyzed. The force constants of the C(SINGLE BOND)C stretching coordinates can be easily corrected by a second-order fit. Thus, only two parameters are needed to reduce the mean error from 21.2 to 1.23%. The errors of other internal coordinates, particulary those including torsional modes, exhibit a larger diversity. The performance of the correction scheme in predicting vibrational spectra is shown for several examples including buckminsterfullerene (C₆₀). © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 2050–2059, 1997     

A semiempirical approach to ligand‐binding affinities: Dependence on the Hamiltonian and corrections

We present a combination of semiempirical quantum‐mechanical (SQM) calculations in the conductor‐like screening model with the MM/GBSA (molecular‐mechanics with generalized Born and surface‐area solvation) method for ligand‐binding affinity calculations. We test three SQM Hamiltonians, AM1, RM1, and PM6, as well as hydrogen‐bond corrections and two different dispersion corrections. As test cases, we use the binding of seven biotin analogues to avidin, nine inhibitors to factor Xa, and nine phenol‐derivatives to ferritin. The results vary somewhat for the three test cases, but a dispersion correction is mandatory to reproduce experimental estimates. On average, AM1 with the DH2 hydrogen‐bond and dispersion corrections gives the best results, which are similar to those of standard MM/GBSA calculations for the same systems. The total time consumption is only 1.3–1.6 times larger than for MM/GBSA. © 2012 Wiley Periodicals, Inc.