scholarly journals Link atom bond length effect in ONIOM excited state calculations

2010 ◽  
Vol 133 (5) ◽  
pp. 054104 ◽  
Author(s):  
Marco Caricato ◽  
Thom Vreven ◽  
Gary W. Trucks ◽  
Michael J. Frisch
Keyword(s):  
Excited State ◽  
Bond Length ◽  
Length Effect ◽  
Link Atom ◽  
Atom Bond

STUDY ON COMPLEXES OF TRYPSIN AND ITS INHIBITORS BY MEANS OF ATOM-BOND ELECTRONEGATIVITY EQUALIZATION METHOD FUSED INTO MOLECULAR MECHANICS (ABEEM/MM)

2007 ◽  
Vol 06 (04) ◽  
pp. 731-746 ◽  
Author(s):  
QING-MEI GUAN ◽  
ZHONG-ZHI YANG
Keyword(s):  
Hydrogen Bond ◽  
Bond Length ◽  
Molecular Mechanics ◽  
Trypsin Inhibitor ◽  
Electrostatic Interactions ◽  
Hydrogen Atoms ◽  
Electronegativity Equalization ◽  
Electronegativity Equalization Method ◽  
Atom Bond ◽  
Equalization Method

Trypsin is one of the most important enzymes and plays important roles in the regulation of biological processes. The newly developed trypsin–inhibitor interaction potential model based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) was employed to study complexes of trypsin and its inhibitors. Some structural properties, including root-mean-square deviations (RMSD) of bond length, bond angle and key dihedral, and coordinated RMS Shifts of atoms and hydrogen bond, were studied using ABEEM/MM method and compared with OPLS-AA force-field. At the same time, comparative study on the charges of the hydrogen atoms at the tail of the ligand was also discussed in order to investigate the effect of hydrogen bond between trypsin and its ligand. This work demonstrates that ABEEM/MM model can well reproduce good structures for these trypsin–inhibitor complexes with rather small RMSD of bond length, bond angles, key dihedrals, and RMS Shifts of atomic coordinates with respect to the experimental crystal structures, compared with the results from the OPLS-AA method. The charges obtained by ABEEM/MM model are in good accordance with those from an ab initio calculation. Moreover, both the polarization and the salt-bridge effects have been taken into account. It is shown that ABEEM charges can properly describe the electrostatic interactions between the protein trypsin and its inhibitors.

Ammonia oxide. I. Geometry and stability

1976 ◽  
Vol 29 (2) ◽  
pp. 231 ◽  
Author(s):  
BT Hart
Keyword(s):  
Excited State ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Bond Length ◽  
Ground State ◽  
Tautomeric Form ◽  
Potential Curve ◽  
Repulsive Potential ◽  
Means Of Production

Ab initio calculations, utilizing Gaussian lobe functions, are reported for the molecule ammonia oxide, NH3O. Results indicate that ammonia oxide has a bound ground state, an abnormally long NO bond length (169 pm) and is 125.9 kJ mol-1 less stable than the tautomeric form hydroxylamine, NH2OH. Possible means of production of the molecule are discussed. The 3E excited state of ammonia oxide was found to have a repulsive potential curve. Possible reasons for this instability are advanced.

The electronic absorption spectra of NH 2 and ND 2

1959 ◽  
Vol 251 (1002) ◽  
pp. 553-602 ◽  
Keyword(s):  
Excited State ◽  
Bond Length ◽  
Absorption Spectra ◽  
Flash Photolysis ◽  
Electronic Absorption Spectra ◽  
Interaction Constant ◽  
Bending Vibration ◽  
Vibronic Structure ◽  
Linear Configuration ◽  
Centrifugal Distortion Constants

The absorption spectra of <super>14</super>NH 2 , <super>15</super>NH 2 and <super>14</super>ND 2 have been photographed in the region 3900 to 8300 A with a 21 ft. concave grating spectrograph. The radicals are produced by the flash photolysis of <super>14</super>NH 3 , <super>15</super>NH 3 and <super>14</super>ND 3 respectively. A detailed study of the <super>14</super>NH 2 - <super>15</super>NH 2 isotope shifts suggests that the molecule has a linear configuration in the excited state and that the spectrum consists of a long progression of the bending vibration in this state. These conclusions have been confirmed by detailed rotational and vibrational analyses of the 14NH2 and 14ND2 spectra. The spectra consist of type C bands for which the transition moment is perpendicular to the plane of the molecule. For NH2, sixteen bands of the progression (0, v'%, 0) <- (0, 0, 0) have been identified with v'% — 3, 4, ..., 18. In addition four bands of a subsidiary progression (1, v'2, 0) <- (0, 0, 0) have been found; these bands derive most of their intensity from a Fermi-type resonance between (0, v'2) 0) and (1, v2 —4, 0) levels in the excited state. The interaction constant W nl is 72 + 3 cm <super>-1</super>. For ND 2 , fourteen bands of the principal progression (v2 — 5 to 18) and one band of the subsidiary progression have been identified. The upper state vibration frequencies w?' and (i)' are 3325 cm <super>-1</super> and 622 cm <super>-1</super> for NH 2 and 2520 cm <super>-1</super> and 422 cm <super>-1</super> for ND 2 respectively. The bending frequencies are unusually low ; moreover, the anharmonicities of the bending vibration are unusually large and negative (x22—11.4 cm <super>-1</super> for NH 2 and 8.1 cm <super>-1</super> for ND 2 ). The origin of the system lies in the region o f 10000 cm <super>-1</super>. Ground-state rotational term values have been derived from observed com bination differences; values for the rotational constants Aooo, B'ooo and Cooo and for the centrifugal distortion constants D"A, D"b and D"0 have been determined. The bond lengths and bond angles for NH 2 and ND 2 agree and are 1.024 + 0.005 A and 103° 20' + 30' respectively. Small spin splittings have been observed. In the excited state an unusual type of vibronic structure has been found. Successive levels of the bending vibration consist alternately of 27, d , T, ... and ... vibronic sub-levels with large vibronic splittings. The origins of the vibronic sub-bands may be represented by the formula yf = Vq—GK2, where G is ~ 27 cm -1 for NH 2 and ~ 19 cm <super>-1</super> for ND 2 . The rotational levels show both spin and A-type doubling. No simple formula has been found to fit the energies o f the II, A, 0 and -T rotational levels; the 27 levels fit the formula F(N) = 1) — D N2(N + 1)2, though with a negative value for D . By extrapolating the B values for the 27 levels to = 0 we obtain B'00o = 8.7 8 cm <super>-1</super> for NH 2 and 4.4 1 cm<super>-1</super> for ND 2 . These values are consistent with a linear configuration with a bond length of 0.97 5 A. The significance of this short bond length is discussed. An explanation of the complex vibronic structure is given. The two combining states are both derived from an electronic II state which is split by electronic-vibrational coupling for the reasons advanced by Renner. A detailed correlation diagram is given. A quantitative treatment of this effect by Pople & Longuet-Higgins gives good agreement with the experimental data.

scholarly journals Measuring Surface Atom Bond Length Contraction in Au and Pt Nanoparticles Using High-Precision STEM Imaging

2013 ◽  
Vol 19 (S2) ◽  
pp. 1688-1689
Author(s):  
A.B. Yankovich ◽  
B. Berkels ◽  
W. Dahmen ◽  
R. Sharpley ◽  
P. Binev ◽  
...  
Keyword(s):  
Bond Length ◽  
High Precision ◽  
Pt Nanoparticles ◽  
Surface Atom ◽  
Length Contraction ◽  
Measuring Surface ◽  
Atom Bond

Extended abstract of a paper presented at Microscopy and Microanalysis 2013 in Indianapolis, Indiana, USA, August 4 – August 8, 2013.

scholarly journals Chlorido(pyridine-κN)(5,10,15,20-tetraphenylporphyrinato-κ4N)cobalt(III) chloroform hemisolvate

2012 ◽  
Vol 68 (8) ◽  
pp. m1104-m1105 ◽  
Author(s):  
Yassin Belghith ◽  
Jean-Claude Daran ◽  
Habib Nasri
Keyword(s):  
Bond Length ◽  
Electron Density ◽  
Title Complex ◽  
Acta Cryst ◽  
Π Interactions ◽  
The Difference ◽  
Difference Fourier ◽  
Atom Bond

In the title complex, [CoCl(C44H28N4)(C5H5N)]·0.5CHCl3or [CoIII(TPP)Cl(py)]·0.5CHCl3(where TPP is the dianion of tetraphenylporphyrin and py is pyridine), the average equatorial cobalt–pyrrole N atom bond length (Co—Np) is 1.958 (7) Å and the axial Co—Cl and Co—Npydistances are 2.2339 (6) and 1.9898 (17) Å, respectively. The tetraphenylporphyrinate dianion exhibits an important nonplanar conformation with major ruffling and saddling distortions. In the crystal, molecules are linkedviaweak C—H...π interactions. In the difference Fourier map, a region of highly disordered electron density was estimated using the SQUEEZE routine [PLATON; Spek (2009),Acta Cryst.D65, 148–155] to be equivalent to one half-molecule of CHCl3per molecule of the complex.

Cyclopentadithiophene derivatives: a step towards an understanding of thiophene copolymer excited state deactivation pathways

2018 ◽  
Vol 2 (1) ◽  
pp. 149-156 ◽  
Author(s):  
João Pina ◽  
Anika Eckert ◽  
Ullrich Scherf ◽  
Adelino M. Galvão ◽  
J. Sérgio Seixas de Melo
Keyword(s):  
Excited State ◽  
Bond Length ◽  
Dihedral Angle ◽  
Stokes Shift ◽  
Length Change ◽  
Large Stokes Shift

In (cis) cyclopentadithiophene, the large Stokes shift is due to a bond length change whereas with α2 (trans) it involves a change in the dihedral angle.

scholarly journals Isomers in the chemistry of iron coordination compounds

2010 ◽  
Vol 8 (5) ◽  
pp. 965-991 ◽  
Author(s):  
Milan Melnik ◽  
Mária Kohútová
Keyword(s):  
Coordination Chemistry ◽  
Bond Length ◽  
Iron Atom ◽  
Coordination Compounds ◽  
Structural Data ◽  
Coordination Complexes ◽  
Oxidation States ◽  
Wide Field ◽  
Iron Coordination ◽  
Atom Bond

AbstractThe coordination chemistry of iron covers a wide field, as shown by a survey covering the crystallographic and structural data of almost one thousand and three hundred coordination complexes. About 6.7% of these complexes exist as isomers and are summarized in this review. Included are distortion (96.6%) and cis — trans (3.4%) isomers. These are discussed in terms of the coordination about the iron atom, bond length and interbond angles. Distortion isomers, differing only by degree of distortion in Fe-L, Fe-L-Fe and L-Fe-L parameters, are the most common. Iron is found in the oxidation states zero, +2 and +3 of which +3 is most common. The stereochemistry around iron centers are tetrahedral, five — coordinated (mostly trigonal — bipyramid) and six — coordinated. The most common ligands have O and N donor sites.

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