Phase Noise Analysis of Time Transfer over White Rabbit-Network Based Optical Fibre Links.

White Rabbit (WR) is an optical fibre-based time-frequency synchronization technology typically used in timekeeping laboratories for distributing time-frequency signals from a reference clock to distant locations. The accuracy of the received signals at the user end can be affected by random noise processes present in the WR network due to the internal electronic components of WR devices. In this paper, we investigate the presence of random noise processes in the WR network. We then study their statistical properties and model the distribution based on experimentally recorded measurements. According to our study, the probability density function (PDF) follows a Gaussian mixture model (GMM) with varying distribution parameters, and the correlation analysis indicates a strong correlation of the phase noise process over the temporal samples. Furthermore, the developed phase noise models have also been verified by comparing them against additional experimental data. Finally, we present the methodology to generate the phase noise process using computer simulations with the PDF and correlation models developed in this work to help algorithm developers and equipment manufacturers make use of our results.

Frequency stabilization of multiple lasers to a reference atomic transition of Rb.

Modern atomic clocks based on the interrogation of an atomic transitions in the optical regions require multiple lasers at different wavelength for producing atomic ions, trapping and laser cooling of neutral atoms or atomic ions. In order to achieve highest efficiency for laser cooling or any other atomic transition, frequencies of each of the lasers involved need to be stabilized by mitigating its drifts or fluctuations arise due to ambient temperature variation or other kind of perturbations. The present article describes simultaneous frequency stabilization of multiple number of lasers, required for production and laser cooling of ytterbium (171Yb) ions, to a reference transition frequency of rubidium (Rb) atoms. In this technique, a diode laser operating at ~ 780 nm is frequency stabilized to one of the Doppler broadening-free absorption peak of rubidium atoms (85Rb) and then used as a reference frequency for calibrating a wavelength meter and subsequent simultaneous frequency stabilization of four lasers operating at different wavelengths.

Carboxyl-catalyzed prototropic rearrangements in histidine peptide radicals upon electron transfer: effects of peptide sequence and conformation.

We report an unusual prototropic rearrangement in gas-phase radicals formed by collisional electron transfer from cesium atoms to protonated peptides HAL, AHL, and ALH at 50 keV. The rearrangement depends on the peptide amino acid sequence and presence or steric accessibility of a free carboxyl group. Upon electron transfer, protonated HAL and ALH rearrange to tautomers that are detected as nondissociated anions in charge-reversal mass spectra. The isomerization is minor in protonated ALH and virtually absent in HAL amide. Electron structure calculations indicate that the gas-phase ions are preferentially protonated in the His imidazole ring and consist of multiple conformers that differ in their hydrogen bonding patterns. Electron transfer to protonated HAL and AHL triggers an exothermic and dynamically barrierless transfer of the carboxyl proton onto the C-2' position of the His ring that occurs on a 120-240 ns time scale. The kinetics of this isomerization are controlled by internal rotations in the radicals to assume conformations favoring the proton transfer. The radical conformations also affect subsequent proton migrations in zwitterionic His imidazoline intermediates that reform the COOH group and result in His ring isomerization. This autocatalytic prototropic rearrangement in gas-phase peptide radicals is analogous to enzyme catalytic reactions involving His and acidic amino acid residues. In contrast to HAL and AHL, the C-2' position is sterically inaccessible in ALH radicals. These radicals undergo proton migrations to the His ring C-5' positions that have moderate energy barriers and are less efficient. RRKM calculations on the combined B3LYP and PMP2/6-311++G(2d,p) potential energy surface of the ground doublet electronic state of the peptide radicals provided rate constants that were quantitatively consistent with the dissociations observed in the gas phase. The formation of minor sequence z(1) and z(2) fragments from AHL was interpreted as occurring in the first excited state of the radical.

Transition metals as electron traps. II. Structures, energetics and electron transfer dissociations of ternary Co, Ni and Zn-peptide complexes in the gas phase.

Transition metal cations Co2+, Ni2+ and Zn2+ form 1 : 1 : 1 ternary complexes with 2,2'-bipyridine (bpy) and peptides in aqueous methanol solutions that have been studied for tripeptides GGG and GGL. Electrospray ionization of these solutions produced singly charged [Metal(bpy)(peptide-H)]+ and doubly charged [Metal(bpy)(peptide)]2+ ions (Metal = metal ion) that underwent charge reduction by glancing collisions with Cs atoms at 50 and 100 keV collision energies. Electron transfer to [Metal(bpy)(peptide)]2+ ions was less than 4.2 eV exoergic and formed abundant fractions of non-dissociated charge-reduced intermediates. Charge-reduced [Metal(bpy)(peptide)]+ ions dissociated by the loss of a hydrogen atom, ammonia, water and ligands that depended on the metal ion. The Ni and Co complexes mainly dissociated by the elimination of ammonia, water, and the peptide ligand. The Zn complex dissociated by the elimination of ammonia and bpy. A sequence-specific fragment was observed only for the Co complex. Electron transfer to [Metal(bpy)(peptide-H)]+ was 0.6-1.6 eV exoergic and formed intermediate radicals that were detected as stable anions after a second electron transfer from Cs. [Metal(bpy)(peptide-H)] neutrals and their anions dissociated by the loss of bpy and peptide ligands with branching ratios that depended on the metal ion. Optimized structures for several spin states, electron transfer and dissociation energies were addressed by combined density functional theory and Møller-Plesset perturbational calculations to aid interpretation of experimental data. The experimentally observed ligand loss and backbone cleavage in charge-reduced [Metal(bpy)(peptide)]+ complexes correlated with the dissociation energies at the present level of theory. The ligand loss in +CR- spectra showed overlap of dissociations in charge-reduced [Metal(bpy)(peptide-H)] complexes and their anionic counterparts which complicated spectra interpretation and correlation with calculated dissociation energies.

Electron-capture-induced dissociation of microsolvated di- and tripeptide monocations: elucidation of fragmentation channels from measurements of negative ions.

The results from an experimental study of bare and microsolvated peptide monocations in high-energy collisions with cesium vapor are reported. Neutral radicals form after electron capture from cesium, which decay by H loss, NH(3) loss, or N-C(alpha) bond cleavage into characteristic z(*) and c fragments. The neutral fragments are converted into negatively charged species in a second collision with cesium and are identified by means of mass spectrometry. For protonated GA (G = glycine, A = alanine), the branching ratio between NH(3) loss and N-C(alpha) bond cleavage is found to strongly depend on the molecule attached (H(2)O, CH(3)CN, CH(3)OH, and 18-crown-6 ether (CE)). Addition of H(2)O and CH(3)OH increases this ratio whereas CH(3)CN and CE decrease it. For protonated AAA ([AAA+H](+)), a similar effect is observed with methanol, while the ratio between the z(1) and z(2) fragment peaks remains unchanged for the bare and microsolvated species. Density functional theory calculations reveal that in the case of [GA+H](+)(CE), the singly occupied molecular orbital is located mainly on the amide group in accordance with the experimental results.

Transition metals as electron traps. I. Structures, energetics, electron capture, and electron-transfer-induced dissociations of ternary copper-peptide complexes in the gas phase.

Electron-induced dissociations of gas-phase ternary copper-2,2'-bipyridine complexes of Gly-Gly-Gly and Gly-Gly-Leu were studied on a time scale ranging from 130 ns to several milliseconds using a combination of charge-reversal ((+)CR(-)) and electron-capture-induced dissociation (ECID) measured on a beam instrument and electron capture dissociation (ECD) measured in a Penning trap. Charge-reduced intermediates were observed on the short time scale in the (+)CR(-) and ECID experiments but not in ECD. Ion dissociations following electron transfer or capture mostly occurred by competitive bpy or peptide ligand loss, whereas peptide backbone fragmentations were suppressed in the presence of the ligated metal ion. Extensive electron structure theory calculations using density functional theory and large basis sets provided optimized structures and energies for the precursor ions, charge-reduced intermediates, and dissociation products. The Cu complexes underwent substantial structure changes upon electron capture. Cu was calculated to be pentacoordinated in the most stable singly charged complexes of the [Cu(peptide-H)bpy](+*) type where it carried a approximately +1 atomic charge. Cu coordination in charge-reduced [Cu(peptide-H)bpy] intermediates depended on the spin state. The themodynamically more stable singlet states had tricoordinated Cu, whereas triplet states had a tetracoordinated Cu. Cu was tricoordinated in stable [Cu(peptide-H)bpy](-*) products of electron transfer. [Cu(peptide)bpy](2+*) complexes contained the peptide ligand in a zwitterionic form while Cu was tetracoordinated. Upon electron capture, Cu was tri- or tetracoordinated in the [Cu(peptide)bpy](+) charge-reduced analogs and the peptide ligands underwent prototropic isomerization to canonical forms. The role of excited singlet and triplet electronic states is assessed.

Photodissociation of protonated tryptophan and alteration of dissociation pathways by complexation with crown ether.

The behavior of protonated tryptophan (TrpH(+)) and its complex with 18-crown-6-ether (CE) after photoexcitation has been explored based on measurements of dissociation lifetimes, fragmentation channels, and absorption spectra using an electrostatic ion storage ring. A recent implementation of pulsed power supplies for the ring elements with microsecond response times allows us to identify the daughter ion fragment masses and to disentangle fragmentation that occurs from excited states immediately after photoexcitation from that occurring on a longer time scale of several microseconds to milliseconds. We find that attachment of crown ether significantly alters the dissociation channels since it renders the pisigma(*)(NH(3)) state inaccessible and hence prevents the N-H bond breakage which is an important fragmentation channel of TrpH(+). As a result, on a long time scale (>10 micros), photoexcited TrpH(+)(CE) decays exponentially whereas TrpH(+) displays a power-law decay. The only ions remaining in the latter case are Trp(+) radical cations with a broad internal energy distribution caused by the departing hydrogen. Large changes in the fragment branching ratios as functions of excitation wavelength between 210 and 290 nm were found for both TrpH(+) and TrpH(+)(CE).

Hidden histidine radical rearrangements upon electron transfer to gas-phase peptide ions. Experimental evidence and theoretical analysis.

Protonated peptides containing histidine or arginine residues and a free carboxyl group (His-Ala-Ile, His-Ala-Leu, Ala-His-Leu, Ala-Ala-His-Ala-Leu, His-Ala-Ala-Ala-Leu, and Arg-Ala-Ile) form stable anions upon collisional double electron transfer from Cs atoms at 50 keV kinetic energies. This unusual behavior is explained by hidden rearrangements occurring in peptide radical intermediates formed by transfer of the first electron. The rearrangements occur on a approximately 120 ns time scale determined by the radical flight time. Analysis of the conformational space for (His-Ala-Ile + H)(+) precursor cations identified two major conformer groups, 1a(+)-1m(+) and 5a(+)-5h(+) , that differed in their H-bonding patterns and were calculated to collectively account for 39% and 60%, respectively, of the gas-phase ions. One-electron reduction in 1a(+) and 5a(+) triggers exothermic hydrogen atom migration from the terminal COOH group onto the His imidazole ring, forming imidazoline radical intermediates. The intermediate from 5a is characterized by its charge and spin distribution as a novel cation radical-COO(-) salt bridge. The intermediate from 1a undergoes spontaneous isomerization by imidazoline N-H migration, re-forming the COOH group and accomplishing exothermic isomerization of the initial (3H)-imidazole radical to a (2H)-imidazole radical. An analogous unimolecular isomerization in simple imidazole and histidine radicals requires activation energies of 150 kJ mol(-1), and its occurrence in 1a and 5a is due to the promoting effect of the proximate COOH group. The rearrangement is substantially reduced in Ala-Leu-His due to an unfavorable spatial orientation of the imidazole and COOH groups and precluded in the absence of a free carboxyl group in His-Ala-Leu amide. In contrast to His-Ala-Ile and Arg-Ala-Ile, protonated Lys-Ala-Ile does not produce stable anions upon double electron transfer. The radical trapping properties of histidine residues are discussed.

Inverse hydrogen migration in arginine-containing peptide ions upon electron transfer.

Collisional electron transfer from gaseous Cs atoms was studied for singly and doubly protonated peptides Gly-Arg (GR) and Ala-Arg (AR) at 50- and 100-keV kinetic energies. Singly protonated GR and AR were discharged to radicals that in part rearranged by migration of a C(alpha) hydrogen atom onto the guanidine group. The C(alpha)-radical isomers formed were detected as stable anions following transfer of a second electron. In addition to the stabilizing rearrangements, the radicals underwent side-chain and backbone dissociations. The latter formed z fragments that were detected as the corresponding anions. Analysis of the (GR + H)(.) radical potential energy surface using electronic structure theory in combination with Rice-Ramsperger-Kassel-Marcus calculations of rate constants indicated that the arginine C(alpha) hydrogen atom was likely to be transferred to the arginine side-chain on the experimental timescale of

A Soret marker band for four-coordinate ferric heme proteins from absorption spectra of isolated Fe(III)-Heme+ and Fe(III)-Heme+(His) ions in vacuo.

In this work, we report the absorption spectra in the Soret band region of isolated Fe(III)-heme+ and Fe(III)-heme+(His) ions in vacuo from action spectroscopy. Fe(III)-heme+ refers to iron(III) coordinated by the dianion of protoporphyrin IX. We find that the absorption of the five-coordinate complex is similar to that of pentacoordinate metmyoglobin variants with hydrophobic binding pockets except for an overall blueshift of about 16 nm. In the case of four-coordinate iron(III), the Soret band is similar to that of five-coordinate iron(III) but much narrower. These spectra serve as a benchmark for theoretical modeling and also serve to identify the coordination state of ferric heme proteins. To our knowledge this is the first unequivocal spectroscopic characterization of isolated 4c ferric heme in the gas phase.

Experimental evidence for an inverse hydrogen migration in arginine radicals.

Radicals formed by electron transfer to protonated arginine have been predicted by theory to undergo an inverse migration of the hydrogen atom from the C(alpha) position to the guanidine carbon atom. Experiments are reported here that confirm that a fraction of arginine and arginine amide radicals undergo such an inverse hydrogen migration. The rearranged arginine and arginine amide C(alpha) radicals are detected as stable anions after charge inversion by collisions with Cs atoms of precursor cations at 3 and 50 keV kinetic energies. RRKM calculations on the B3-PMP2/aug-cc-pVTZ potential energy surface indicate that arginine radicals undergo rapid rotations of the side chain to reach conformations suitable for C(alpha)-H transfer, which is calculated to be fast (k > 10(9) s(-1)) in radicals formed by electron transfer. By contrast, H-atom transfer from the guanidine group onto the carboxyl or amide C=O groups is >50 times slower than the C(alpha)-H atom migration. The guanidine group in arginine radicals is predicted to be a poor hydrogen-atom donor but a good H-atom acceptor and thus can be viewed as a radical trap. This property can explain the frequent observation of nondissociating cation radicals in electron capture and electron transfer mass spectra of arginine-containing peptides.

A new technique for time-resolved daughter ion mass spectrometry on the microsecond to millisecond time scale using an electrostatic ion storage ring.

A new method for time-resolved daughter ion mass spectrometry is presented, based on the electrostatic ion storage ring in Aarhus, ELISA. Ions with high internal energy, e.g., as a result of photoexcitation, dissociate and the yield of neutrals is monitored as a function of time. This gives information on lifetimes in the microsecond to millisecond time range but no information on the fragment masses. To determine the dissociation channels, we have introduced pulsed supplies with switching times of a few microseconds. This allows rapid switching from storage of parent ions to storage of daughter ions, which are dumped into a detector after a number of revolutions in the ring. A fragment mass spectrum is obtained by monitoring the daughter ion signal as a function of the ring voltages. This technique allows identification of the dissociation channels and determination of the time dependent competition between these channels.

Dianions of 7,7,8,8-tetracyano-p-quinodimethane and perfluorinated tetracyanoquinodimethane: information on excited states from lifetime measurements in an electrostatic storage ring and optical absorption spectroscopy.

We have developed an experimental technique that allows us to study the physics of short lived molecular dianions in the gas phase. It is based on the formation of monoanions via electrospray ionization, acceleration of these ions to keV energies, and subsequent electron capture in a sodium vapor cell. The dianions are stored in an electrostatic ion storage ring in which they circulate with revolution times on the order of 100 micros. This enables lifetime studies in a time regime covering five orders of magnitude, 10(-5)-1 s. We have produced dianions of 7,7,8,8-tetracyano-p-quinodimethane and 2,3,5,6-tetrafluoro-7,7,8,8-tetracyano-p-quinodimethane (TCNQ-F(4)) and measured their lifetimes with respect to electron autodetachment. Our data indicate that most of the dianions were initially formed in electronically excited states in the electron transfer process. Two levels of excitation were identified by spectroscopy on the dianion of TCNQ-F(4), and the absorption spectrum was compared with spectra obtained from spectroelectrochemistry of TCNQ-F(4) in acetonitrile solution.

On the mechanism of electron-capture-induced dissociation of peptide dications from 15n-labeling and crown-ether complexation.

15N-labeling of di- and tripeptides reveals that electron capture to doubly protonated peptides results almost exclusively in ammonia loss from the N-terminal end, which clearly shows that a significant fraction of electron capture occurs at this end. In accordance with this finding, the competing channel of N-Calpha bond breakage leads to z+* ions and neutral c fragments after electron capture to small dications. In larger peptides that live long enough for internal proton exchanges to occur, c+ ions are also formed and in some cases in dominant yield. Attachment of one or two crown ethers to ammonium groups is likely to reduce the probability of proton transfer, which enhances the formation of z+* relative to c+. The total yield of z+* and c+ is, however, more or less unchanged, which indicates that proton transfer or hydrogen transfer from a NH3 group to the amide group is not required for the N-Calpha bond breakage.

Photophysical behaviour of 4-(imidazole-1-yl) phenol and its complexation with beta-cyclodextrin in ground and excited states.

This paper mainly dwells on photophysics of 4-(imidazole-1-yl) phenol (IDP) in different solvents and temperatures from the investigations of absorption, emission and laser flash photolysis and also on the nature of complexation with beta-cyclodextrin (CD) in ground and excited states. IDP makes 1:1 inclusion complex with beta-CD in ground, excited singlet and also in triplet states. The orientation of complex could be ascertained as imidazole moiety stays inside the cavity with phenol moiety stays in the bulk. A proposed energy level scheme unveils that vibronic interaction and spin-orbit interaction are found to be active differently in aprotic and protic solvents.

Photophysics of 4-(N,N-dimethylamino)cinnamaldehyde/ alpha-cyclodextrin inclusion complex.

This paper reports the probing of alpha-cyclodextrin (alpha-CD) cavities with the help of dual emission properties of 4-N,N dimethylamino cinnamaldehyde (DMACA) in aqueous solution. An interesting feature could be observed that due to 1:1 complexation DMACA is encapsulated within alpha-CD in two distinctly different types of orientation as revealed from the relative positions and the intensity of locally excited state localized within donor and acceptor subunits (LE) and twisted intramolecular charge transfer (TICT) bands. In one situation the dimethylamino group is directed towards the larger rim of the cavity and in other the orientation is just the opposite. The different types of complexes were found to be excited selectively in different wavelength regions.