Chemical Physics Letters (v.523, #C)
Editorial Board (IFC).
The separation of overlapping transitions in β -carotene with broadband 2D electronic spectroscopy by Tessa R. Calhoun; Jeffrey A. Davis; Matthew W. Graham; Graham R. Fleming (1-5).
Display Omitted► β-carotene at 77 K was studied with broadband 2D electronic spectroscopy. ► Overlapping transitions in the energetic region associated with S∗ were resolved. ► Dynamic lineshapes consistent with ISRS were observed and modeled. ► A nonrephasing signal of unknown origin was detected at long times.Broadband 2D electronic spectroscopy is applied to β -carotene, revealing new insight into the excited state dynamics of carotenoids by exploring the full energetic range encompassing the S 0 → S 2 and S 1 → S 1 n transitions at 77 K. Multiple signals are observed in the regime associated with the proposed S∗ state and isolated through separate analysis of rephasing and nonrephasing contributions. Peaks in rephasing pathways display dynamic lineshapes characteristic of coupling to high energy vibrational modes, and simulation with a simple model supports their assignment to impulsive stimulated Raman scattering. A signal persisting beyond 10 ps in the nonrephasing spectra is still under investigation.
Tantalum atom reactions with ammonia: Matrix infrared spectra and DFT calculations of the H2TaNH and H2Ta(NH2)2 molecules by Xing Liu; Xuefeng Wang; Bing Xu; Lester Andrews (6-10).
The tantalum atom reaction with one ammonia molecule to give imido complex H2TaNH and with two ammonia molecules to give amido complex H2Ta(NH2)2.Display Omitted► Tantalum atoms react with ammonia to form the metal-ammonia complexes. ► These complexes rearrange to form the imido and amido complexes. ► Isotopic substitutions and DFT frequency calculations are used for identification. ► Reaction mechanism is investigated theoretically.Laser-ablated tantalum atoms react with ammonia to form the metal-ammonia complexes Ta(NH3) and Ta(NH3)2 spontaneously on annealing. These complexes underwent photochemical rearrangement to form the imido molecule H2TaNH and amido complex H2Ta(NH2)2. The reaction products have been identified by isotopic substitutions as well as density functional theoretical frequency calculations. In addition, reaction mechanism of the possible reaction paths for these reactions is discussed.
NMR characterization of substituent effects in cation–π interactions by Fareed Bhasha Sayyed; Cherumuttathu H. Suresh (11-14).
Display Omitted► Substituent effects in C6H5X…M+ (M+ = Li+, Na+, K+, and NH 4 + ) complexes are studied. ► Isotropic nuclear magnetic shielding constants (σ) are proposed as a measure of substituent effects. ► The dependence of cation–π distance (R) on the σ was studied using the σ vs. R plots.Substituent effects in C6H5X…M+ (M+ = Li+, Na+, K+, and NH 4 + ) systems have been characterized using isotropic nuclear magnetic shielding constants (σ). Good linear relationship between σ and the Hammett substituent constant σ p is established which suggests that the substituent effects can be quantified by NMR experiments. Irrespective of the electronic nature of X, meta carbons, and all the hydrogens are always deshielded and this property is useful for detecting cation–π interaction. The σ-scan plots revealed that the deshielding effect of the cation on the aromatic ring is significant even at large cation–π distance (∼4.5 Å).
Comparison of rotationally inelastic rate constants for Li 2 A 1 Σ u + ( v i = 5 , j i = 30 ) + Ne measured using pulsed and cw lasers by M. Rosenberry; R. Marhatta; B. Stewart (15-19).
Display Omitted► Pulsed and cw laser excitation of a molecule lead to equivalent rate constants. ► Differences in the velocity distributions lead the pulsed values to be slightly (13%) higher. ► This difference is confirmed by quasiclassical trajectories run on an ab initio surface.We have measured rotationally inelastic rate constants for the process Li 2 ∗ A 1 Σ u + ( v i = 5 , j i = 30 ) + Ne → Li 2 ∗ A 1 Σ u + ( v f = 5 , j f ) + Ne using pulsed laser excitation and compared them to values previously measured using cw laser excitation, applying uniform analysis techniques to both sets of data. We compare the experimental results with rate constants calculated from quasiclassical trajectories on an ab initio potential energy surface, finding that the two experimental methods give consistent results when the different distributions of excited-state collision speeds are taken into account.
The hydrogen-bridged radical cation [NH2C＝O⋯H⋯O＝CHCH3] •+ and its dissociation by proton-transport catalysis by Karl J. Jobst; Johan K. Terlouw (20-24).
Tandem mass spectrometry and model chemistry calculations show that ethyloxamate ions (EOX-1) cleanly generate HBRC-1, whose dissociation by loss of CH3CO • involves proton-transport catalysis (PTC).Display Omitted► Decarbonylation of ionized ethyl oxamate cleanly yields the title ion (HBRC-1) in high yield. ► Ions HBRC-1 lose CH3C＝O • by a mechanism that involves proton-transport catalysis (PTC). ► The PTC mechanism is supported by D-labeling experiments and computational chemistry.The title ion (HBRC-1) is an easily accessible hydrogen-bridged radical cation when generated by the decarbonylation of ionized ethyl oxamate, NH2COCOOC2H5.Tandem mass spectrometry experiments and CBS-QB3 model chemistry calculations agree that HBRC-1 dissociates into HC(OH)NH2 + + CH3CO • by proton-transport catalysis. Its CH3CHO component catalyzes the isomerization NH2–C–OH •+ → NH2C(O)H •+ and the ensuing intermediate [NH2C(O)H⋯OCHCH3] •+ loses CH3CO • by a facile proton transfer.In support of this, lactamide ions ND2C(O)CH(OD)CH3 •+ dissociate into DC(OH)ND2 + + CH3CO • via the HBRC-1 isotopologue [ND2CO⋯D⋯OCHCH3] •+. HBRC-1 also plays a key role in the decarbonylation of its isomer ionized urethan, NH2COOC2H5.
Unconventional ionic hydrogen bonds: CH+⋯π (CC) binding energies and structures of benzene+• (acetylene)1–4 clusters by Abdel-Rahman Soliman; Ahmed M. Hamid; Samuel A. Abrash; M. Samy El-Shall (25-33).
Condensation of acetylene onto the benzene radical cation results in a concerted charge transfer – cyclization process generating a benzene ring.Display Omitted► Rapid condensation of acetylene onto the benzene cation in the gas phase at 120–140 K. ► Weak binding energies of the four acetylene molecules to the benzene cation (3–4 kcal/mol). ► Associative charge transfer activates the cyclization of three acetylene molecules to form a benzene molecule.Rapid condensation of acetylene onto the benzene cation with the addition of up to eight acetylene molecules is observed in the gas phase at 120–140 K forming the C6D6 •+(C2H2) n clusters. The binding energies and entropy changes of the stepwise condensation of the first four acetylene molecules onto the benzene cation have been measured and correlated with the calculated lowest energy isomers. The measured binding energies (3–4 kcal/mol) reflect weak charge-induced dipole and (benzene) C―Hδ+ ⋯π CC (acetylene) hydrogen bonding interactions. Associative charge transfer is suggested to activate the cyclization of three acetylene molecules to form a benzene molecule (C6H6).
O-atom exchange in O(3P) + H2O(1A1) collisions by Matthew Braunstein; Patrick F. Conforti (34-38).
Display Omitted► O(3P) + H2O(1A1) global potentials are used to explore two new reaction paths. ► Both cross a D2h rhombus point, with zero gradient and two imaginary frequencies. ► One frequency motion leads to O + H2O, while the second motion leads to OH + OH. ► In each case, an O-atom is exchanged. ► Cross sections and rate constants are computed for these processes.Global potential energy surfaces for the three lowest electronic triplet states of O(3P) + H2O(1A1) are used to explore two unusual reaction pathways, not previously identified. Both pathways go through a D2h rhombus geometry, with zero potential gradient and two imaginary frequencies. Motion along one imaginary frequency leads to O + H2O, while motion along the other leads to OH + OH. In each case, an O-atom is exchanged. Classical trajectory methods are used to compute exchange cross sections up to 11 km s−1. Transition state theory rate constants for O-atom exchange processes are also computed.
Theoretical study on microhydration of SeO 4 2 - : On the number of water molecules necessary to stabilize the dianion by Arup Kumar Pathak (39-42).
At least one water molecule is necessary to stabilize the dianion in the gas phase against spontaneous electron loss.Instability of bare SeO 4 2 - is predicted based on microscopic theory.Microscopic theory based expression provides a route to obtain the VDE for a wide range of cluster sizes including the bulk.Display Omitted► Microhydration of SeO 4 2 - · n H 2 O clusters are studied at B3LYP/Aug-cc-pvtz level. ► Higher size cluster (n > 3) contains cyclic water ring. ► One water molecule is necessary to stabilize the dianion against electron loss. ► Microscopic theory based expression predicts the instability of bare SeO 4 2 - . ► VDE for a wide range of cluster sizes including the bulk is extracted.Microhydration of SeO 4 2 - · n H 2 O (n = 1–5) clusters are reported at B3LYP/Aug-cc-pvtz level of theory. Lower size hydrated clusters are stabilized by only double-hydrogen-bonding arrangements and the most stable conformer for higher size cluster (n > 3) contains a cyclic water ring. It is observed that at least one water molecule is necessary to stabilize the dianion in the gas phase against spontaneous electron loss. The microscopic theory based expression provides a route to predict the instability of bare SeO 4 2 - and to obtain the VDE for a wide range of cluster sizes including the bulk from the knowledge of the same for a few stable hydrated clusters.
A theoretical contribution characterizing a potentially new molecular species: MgAs by Ana Paula de Lima Batista; Fernando R. Ornellas (43-48).
Display Omitted► New molecular species: MgAs. ► High-level MCSCF/MRCI/aV5Z investigation. ► Potential energy curves and spectroscopic constants. ► Transition moments; transition probabilities; radiative lifetimes. ► Spin–orbit interaction; relativistic states.A new molecular species, MgAs, is investigated theoretically for the first time at the CASSCF/MRCI level using quintuple-zeta quality basis sets. Potential energy curves for the lowest-lying electronic states are presented as well as the associated spectroscopic constants. Dipole and transition moment functions for selected states complement this characterization. Estimates of transition probabilities and radiative lifetimes for the most important transitions are also reported. The effect of spin–orbit interactions is clearly reflected on the potential energy curves. Comparisons with BeAs, BeN, and BeP are made where pertinent.
Geometric phase and parity-violating energy difference locking of chiral molecules by H.C. Peñate-Rodríguez; P. Bargueño; S. Miret-Artés (49-53).
Display Omitted► We study geometric phases for parity violating chiral molecules. ► We study the Hamiltonian dynamics in terms of canonically conjugate variables. ► We show signatures of parity violation-locking both in the geometric phase and in the interference between chiral states. ► The effects of mean-field interactions in the geometric phase are briefly discussed.Geometric phases within a canonical formulation of chiral molecules are analyzed paying special attention to the fundamental role played by the parity violating energy difference. We study the Hamiltonian dynamics in terms of canonically conjugate variables, showing how parity-violating energy difference could be locked (PVED-locking) by means of a circularly polarized electric field. Signatures of this locking are predicted to occur both in the geometric phase and in the interference between chiral states.
Isomer-resolved dissociation of small carbon cluster cations, C7 +–C10 + by Kiichirou Koyasu; Tomohiro Ohtaki; Noriaki Hori; Fuminori Misaizu (54-59).
Display Omitted► Small carbon cluster cations consist of linear and cyclic isomers. ► Isomer-resolved dissociation reactions are applied to the isomers cations. ► Coexisting linear and cyclic isomers were separated with ion mobility spectrometry. ► Separated isomers show different dissociation channels depending on the structures. ► The difference between the two fragment distributions implies different mechanisms.Isomer-resolved multiphoton dissociation (PD) with 3.5 eV and collision-induced dissociation (CID) were applied to small carbon cluster cations, C n + (n = 7–10), to investigate correlations between the isomer structures and dissociation reactivities. Linear and cyclic isomers, which coexist in this size range, were separated by ion mobility spectrometry using a home-made drift cell. The linear isomers mainly produced C3-loss fragments, while cyclic ones showed C2-loss as well as C3-loss products. The C2-loss products were predominantly observed by PD, whereas comparable amounts of C2- and C3-loss products were observed by CID. The range of the excitation energy of CID was overlapped with that of PD, whereas the former range was wider than the latter. Plausible origins of the difference between the fragment distributions from the cyclic and linear isomers are discussed in terms of the energetics of the fragment ions.
Tuned long-range corrected density functional theory method for evaluating the second hyperpolarizabilities of open-shell singlet metal–metal bonded systems by Hitoshi Fukui; Yudai Inoue; Ryohei Kishi; Yasuteru Shigeta; Benoît Champagne; Masayoshi Nakano (60-64).
Display Omitted► The performance of the LC-UBLYP method for γ in metal–metal bonded systems. ► Significant dependence of γ on the range separating parameter (μ). ► The optimal μ lies between 0.7−0.9 bohr−1.The range separating parameter (μ) in the long-range corrected spin-unrestricted BLYP (LC-UBLYP) method is tuned so as to reproduce the second hyperpolarizabilities (γ) of several open-shell singlet metal–metal bonded systems calculated using the strongly electron-correlated spin-unrestricted coupled cluster singles, doubles and perturbative triples [UCCSD(T)] method. For these systems, μ values ranging between 0.7 and 0.9 bohr−1 provide a reliable description of the bond length dependence of γ in the bond length region where γ is enhanced by the contribution of dσ electrons with an intermediate open-shell character.
Theoretical study of intermolecular magnetic interaction of chromium(V)–nitrido complex self-assembly with tetradentate Schiff base ligand by Naoki Matsuoka; Naoki Yoshioka (65-68).
Display Omitted► Magnetic property of chromium(V)–nitrido complex self-assemblies was elucidated. ► Close contact between chromium(V) and nitrido site caused magnetic interaction. ► The magnetic interaction is explained by the large spin polarization in nitrido site.A theoretical study of the intermolecular magnetic interaction of [CrN(salpn)] is discussed based on DFT calculations. The close contact between the 2p orbitals on the axial nitrogen and other 3d orbitals besides the 3d xy orbital on the adjacent chromium is effective for ferromagnetic coupling. The magnetic interaction is rationally explained by the significantly large spin polarization of the axial nitrogen.
The Yang–Yang anomaly in liquid–liquid criticality: Experimental evidence from adiabatic scanning calorimetry by Patricia Losada-Pérez; Chandra Shekhar Pati Tripathi; Jan Leys; Claudio A. Cerdeiriña; Christ Glorieux; Jan Thoen (69-73).
Display Omitted► We detect the Yang–Yang anomaly in liquid–liquid criticality for the first time. ► Such anomaly as an impurity induced effect is ruled out. ► Results are in agreement with complete scaling predictions. ► Molecular size may not be the only microscopic parameter driving asymmetry. ► Exactly soluble models to account for the Yang–Yang anomaly are called for.Using adiabatic scanning calorimetry, we have found the first experimental evidence of the Yang–Yang anomaly in liquid–liquid criticality from high-resolution two-phase isobaric heat capacity measurements for the binary mixture 3-pentanol + nitromethane. The results suggest a rather strong effect. The critical amplitude of the partial molar heat capacity is higher for the component with larger molecular volume, in accordance with the predictions of complete scaling as obtained from the customary observed asymmetric behavior of the coexistence-curve diameter. This consolidates complete scaling as the true formulation of fluid–fluid criticality. The quantitative analysis indicates that molecular size is not the only microscopic factor at play in asymmetric liquid–liquid criticality.
Phase recognition by lattice phonon Raman spectra: The triclinic structure of the organic semiconductor dibenzo-tetrathiafulvalene by Aldo Brillante; Ivano Bilotti; Raffaele Guido Della Valle; Elisabetta Venuti; Marta Mas-Torrent; Concepció Rovira; Yoshiro Yamashita (74-77).
Display Omitted► Study of polymorphs in the organic semiconductor dibenzo-tetrathiafulvalene (DB-TTF). ► A working example of phase recognition by lattice phonon Raman spectroscopy is presented. ► Exemplary case of coexistence of crystal phases.We present a working example of phase recognition by lattice phonon Raman spectroscopy, a technique which has proved to be a powerful tool for identifying new polymorphs. The spectra show that a newly resolved triclinic structure of the organic semiconductor dibenzo-tetrathiafulvalene (DB-TTF) is one of its four polymorphic modifications, labeled the δ-phase, which was previously identified only from spectroscopic data. The now available XRD data allow for the computation of the minimum potential energy structure. Calculated density and energy of the triclinic polymorph are found to be very close to the previously identified β polymorph. These similarities account for the often encountered co-existence of the β and δ crystal phases.
Formation dynamics of FeN thin films on Cu(100) by Dodi Heryadi; Udo Schwingenschlögl (78-82).
Display Omitted► Ab initio molecular dynamics simulations of iron nitride formation on Cu(100). ► Iron nitride layers exhibit a p4gm(2 × 2) reconstruction and order ferromagnetically. ► The magnetization trend follows the experimental behavior.To investigate the structural and magnetic properties of thin films of FeN we have performed ab initio molecular dynamics simulations of their formation on Cu(100) substrates. The iron nitride layers exhibit a p4gm(2 × 2) reconstruction and order ferromagnetically in agreement with experiment. We establish the dynamics and time scale of the film formation as a function of the film thickness. The process is split in two phases: formation of almost flat FeN layers and optimization of the distance to the substrate. Our calculated magnetic moments are 1.67 μB, 2.14 μB, and 2.21 μB for one, two, and three monolayers of iron nitride.
Electronic transmutation: Boron acquiring an extra electron becomes ‘carbon’ by Jared K. Olson; Alexander I. Boldyrev (83-86).
Display Omitted► We propose a concept of electronic transmutation. ► This concept may have a significant effect on predicting new chemical compounds. ► Another outcome of this concept will be the simplification of teaching chemistry. ► We conducted an unbiased search for global minimum structures of Li2B2H6. ► The Li2B2H6 molecule is isostructural to the C2H6 ethane molecule.We propose a concept of electronic transmutation. According to this concept, elements, by acquiring an extra electron, begin to have the chemical bonding and geometric structure properties of compounds composed of neighboring elements. We demonstrate that boron, by acquiring an extra electron in boron–hydrogen compounds, forms molecular analogs of those of saturated hydrocarbons. We show by the means of quantum chemistry that the Li2B2H6 molecule in the most stable geometric form has the B2H6 2− kernel, which is isostructural to the C2H6 ethane molecule. We believe that this concept may have a significant effect on predicting new chemical compounds.
Laser heating effect on Raman spectra of styrene–butadiene rubber/multiwalled carbon nanotube nanocomposites by Xinlei Yan; Yasutaka Kitahama; Harumi Sato; Toshiaki Suzuki; Xiaoxia Han; Tamitake Itoh; Liliane Bokobza; Yukihiro Ozaki (87-91).
Display Omitted► ID/IG in SBR/MWCNTs sample sharply decreased with laser heating. ► G band shift in nanocomposites was weaker than that in MWCNTs. ► Self-rearrangement of MWCNTs in nanocomposites was detected with laser heating. ► Mechanical compression plays a role on the temperature effect of MWCNTs.The laser heating effect on MWCNTs in styrene–butadiene rubber/multiwalled carbon nanotube (SBR/MWCNT) composites were studied by Raman spectra. The intensity ratio of the D band to G band (I D/I G) of SBR/MWCNT composites largely decreased with temperature. This indicates the self-rearranging behavior of MWCNTs in the SBR/MWCNTs system during temperature increase. In addition, the temperature-dependent downward shift of the G band of SBR/MWCNT composites was smaller than that of MWCNTs samples. The self-rearrangement of MWCNTs in SBR/MWCNT composites and a mechanical compression were explained as two possible reasons for the different behavior of the G band shift.
General formula for accurate calculation of halofullerenes polarizability by D.Sh. Sabirov; R.R. Garipova; R.G. Bulgakov (92-97).
Display Omitted► The polarizability of C60Hal n does not grows up linearly with n increase. ► This phenomenon called the depression of polarizability is typical for various classes of halofullerenes. ► General formula for calculation of halofullerenes polarizability has been found.At the first time mean polarizabilities of fluoro-, chloro-, bromofullerenes have been calculated. The dependences of halofullerenes polarizabilities on the structure and the number of halogen atoms in a molecule have been analyzed. The phenomenon of polarizability depression is typical for all compounds under study. General formula for calculation of all classes of halofullerenes mean polarizabilities has been derived based on polarizability depression. Its applicability to related compounds (C70 fullerene choro-derivatives and hypothetical iodofullerenes) has been shown.
Tunable band gap and magnetism in C2 x -(BN) y sheets and ribbons by Chun Tang; Liangzhi Kou; Changfeng Chen (98-103).
Display Omitted► 2-D zigzag C-BN show distinct magnetism from 1-D ribbons due to orbit hybridization. ► They also show different band-gap variation due to the distinct magnetic properties. ► The band gaps of armchair C-BN sheets and ribbons show distinct scaling rules.We predict using first-principles calculations that recently synthesized C-BN nanostructures exhibit rich magnetic and electronic properties that are sensitive to system dimensionality and chirality. Due to different C-B(N) pz-orbital hybridization at the interface, two-dimensional zigzag C-BN sheets and one-dimensional zigzag nanoribbons show weak and strong magnetism respectively. Moreover, the band gap of the zigzag ribbons shows strong sensitivity to the edge magnetism and the BN concentration. For armchair systems, the band gap of the C-BN sheets and ribbons exhibits distinct variation trends with the changing BN concentration, correlating with the width of the adjacent graphene nanoribbon.
Ultrafast third-order nonlinear optical properties of graphene in aqueous solution and polyvinyl alcohol film by Saisai Chu; Shufeng Wang; Qihuang Gong (104-106).
Display Omitted► Ultrafast third-order nonlinear optics of graphene was investigated by OKE. ► γ c Of graphene was determined to be 3.4 × 10−32 esu per carbon atom. ► The χ (3) of graphene/PVA film (OD = 0.52) was measured 3.1 × 10−12 esu.The ultrafast third-order nonlinear optical properties of graphene in both suspension and film status are studied using femtosecond time resolved optical Kerr gate technique at 800 nm. The third-order nonlinear optical susceptibility is 4.2 × 10−14 esu for solution of 0.010 mg/ml. The corresponding second-order hyperpolarizability is 3.4 × 10−32 esu per carbon atom in graphene, which is the largest among the carbon family. The graphene embed in the polymer matrix of polyvinyl alcohol film (OD = 0.43) exhibits strong ultrafast nonlinear optical response of 3.3 × 10−12 esu and shows its potential application in nonlinear optics.
Revealing oxidation kinetics of dielectric-embedded Ag nanoparticles via in situ optical microspectroscopy by J.A. Jiménez; M. Sendova; K. McAlpine (107-112).
Display Omitted► Real-time assessment of oxidation kinetics of dielectric-embedded Ag nanoparticles. ► Energy barrier determination from the temperature dependence of the process. ► Connection with underlying mechanism. ► Research opportunities opened with relevance to both materials and biological sciences.The oxidation kinetics of Ag nanoparticles (NPs) embedded in an aluminum oxide film deposited on quartz have been assessed via an in situ real-time monitoring of plasmonic evolution during thermal processing in air. A temperature-dependent exponential decay in the peak intensity of Ag NPs’ absorption was revealed, which was analyzed through first-order kinetics. An activation energy of 3.28 (±0.27) × 104 J mol−1 was estimated in good agreement with the oxidative dissolution of similar-sized Ag NPs in liquid phase reported by Ho et al. . Results are discussed in the context of mechanistic parallelisms and physico-chemical interactions in the air-atmosphere/nanocomposite-film/substrate system.
Thermal chemiluminescence spectroscopy of amino acids and its salts using a multichannel Fourier-transform spectrometer by Taishi Yamada; Taketo Karakisawa; Masahiko Sekine; Hiroshi Ishii; Chikahiro Satoh; Keith R. Millington; Munetaka Nakata (113-119).
Display Omitted► Luminescence spectroscopy was applied to glycine, alanine, serine and threonine. ► Their dicyclohexylamine salts showed strong thermal luminescence bands. ► CH3 and OH groups on the side chain induced blue and red shifts, respectively. ► Luminescence spectroscopy could be established as a new molecular spectroscopy.The thermal chemiluminescence spectra of the dicyclohexylamine (DCHA) salts of glycine, alanine, serine, and threonine were measured with a multichannel Fourier-transform chemiluminescence (FT-CL) spectrometer. The zwitterionic amino acids themselves are non-luminescent because their amine groups are protonated, whereas the corresponding DCHA salts show strong emission in the presence of oxygen because their NH2 groups are free. It was found that the CH3 and OH groups on the side chain caused red and blue shifts, respectively, suggesting that thermal luminescence spectroscopy using an FT-CL spectrometer can be used to identify the presence of electron donating or withdrawing groups in chemiluminescent molecules.
Remarkable hydrogen bonding in the radical anions of guanine–cytosine and adenine–thymine by Bin Peng; Shane R. McNew; Qian-Shu Li; Yaoming Xie; Henry F. Schaefer (120-123).
Display Omitted► The capture of an electron substantially changes hydrogen bonding. ► The base pair anions [GC]− and [AT]− may be described as G[C−] and A[T−]. ► DNA base pairs are electron trappers.Capture of an electron by either DNA base pair results in a major structural reorganization. One of the peripheral hydrogen bonds is significantly lengthened (0.22 Å in GC−) and the other significantly shortened (0.30 Å in AT−). These striking structural shifts are predicted by the MP2 method. We argue that the correct electronic description of the two anions is G[C−] and A[T−], displaying hydrogen bonding between the neutral purine base and the pyrimidine radical anion. This hypothesis is tested via higher level studies of thymine and its radical anion. The experimental conformation or denial of these predictions will provide a major step in our understanding of the structures of biomolecules.
Modulations in restricted amide rotation by steric induced conformational trapping by V.V. Krishnan; William B. Thompson; Joy J. Goto; Kalyani Maitra; Santanu Maitra (124-127).
Display Omitted► Steric induced modulation of restricted amide rotation. ► Two-site chemical exchange to a three-site exchange mechanism. ► Variable temperature NMR, 2D exchange NMR spectroscopy and molecular mechanics calculations.The rotation around the amide bond in N,N-diethyl-m-toluamide (m-DEET) has been studied extensively and often used in laboratory instructions to demonstrate the phenomenon of chemical exchange. Herein, we show that a simple modification to N,N-diethyl-o-toluamide (o-DEET) significantly alters the dynamics of the restricted rotation around the amide bond due to steric interactions between the ring methyl group and the two N-ethyl groups. This alters the classic two-site exchange due to restricted rotation around the amide bond, to a three-site exchange, with the third conformation trapped at a higher-energy state compared to the other two. This often overlooked phenomenon is elucidated using variable-temperature NMR, two-dimensional exchange spectroscopy and molecular modeling studies.
Development of the four-body corrected fragment molecular orbital (FMO4) method by Tatsuya Nakano; Yuji Mochizuki; Katsumi Yamashita; Chiduru Watanabe; Kaori Fukuzawa; Katsunori Segawa; Yoshio Okiyama; Takayuki Tsukamoto; Shigenori Tanaka (128-133).
Display Omitted► The four-body corrected fragment molecular orbital (FMO4) scheme has been implemented. ► This protocol was usable for a nonconventional fragmentation by separating main and side chains of amino acid residues. ► The HIV-1 protease complex with lopinavir was calculated at the FMO4-MP2/6-31G level. ► This job was completed in 1.4 h with 1024 processors of the Earth Simulator.The four-body corrected fragment molecular orbital (FMO4) method was implemented at the second-order Møller–Plesset perturbation (MP2) level. A series of accuracy tests relative to the previous two-body and three-body treatments were performed. As expected, FMO4 provided better accuracy in total energies in comparison with the reference values by regular MO calculations. A nonconventional fragmentation by separating main and side chains in amino acid residues was examined for Ala-pentamer and Chignolin, where the four-body corrections were shown to be substantial. A large complex of HIV-1 protease (total 198 residues) with lopinavir was calculated as well. Furthermore, this new FMO scheme was successfully applied to adamantane-shaped clusters with three-dimensional bonding framework.
Electron wave packet modeling of chemical bonding: Floating and breathing minimal packets with perfect-pairing valence-bond spin coupling by Koji Ando (134-138).
Display Omitted► We examine a simple wave packet modeling of electrons in chemical bonding. ► In particular, we employ floating and breathing minimal Gaussian wave packets. ► The antisymmetry is dealt with by non-orthogonal perfect-pairing valence-bond theory. ► The model is found to give accurate potential energy surfaces of small molecules. ► A simple core pseudo-potential properly models core–valence interactions.A simple wave packet (WP) modeling of electrons in chemical bonding is examined. It is found that floating and breathing minimal Gaussian WPs with fully non-orthogonal perfect-pairing valence-bond spin coupling yield the ground state potential energy surfaces of LiH, BeH2, CH2, and H2O molecules of comparable quality to a high-level ab initio electron-correlated calculations. A simple form of core pseudo-potential with two parameters is shown to give proper modeling of core–valence interactions.
Fast protocol for equilibration of entangled and branched polymer chains by Yelena R. Sliozberg; Jan W. Andzelm (139-143).
Display Omitted► Efficient algorithm for equilibration of entangled polymers of any architecture developed. ► Our DPD-push-off method is fast and simple to implement with MD parallel simulators. ► DPD-push-off is computationally competitive to other equilibration techniques. ► DPD-push-off is suitable for polymers of any complex architecture.Direct brute-force equilibration of well-entangled polymers is beyond the reach of the modern computational power because of slow reptation dynamics exhibited by high molecular weight chains. We have introduced a fast protocol to prepare well-equilibrated entangled polymer melts of various architectures. A soft, DPD-like potential is used to quickly equilibrate the melt at intermediate length-scale following with a replacement of the DPD potential with Lennard–Jones potential. The equilibrated structure is then subjected to a short MD simulation run that relaxes the melt configuration at the short length-scale. The topological characteristics of the final melt structure are excellent, and the method found to be computationally competitive to other state-of-the-art equilibration techniques.
Evans hole in internal modes IR spectrum of WO 3 F 3 3 - ions in (NH4)3WO3F3 crystal by Ju.V. Gerasimova; A.N. Vtyurin (144-147).
Display Omitted► Evans holes were first found in IR absorption spectra of ionic crystal (NH4)3WO3F3. ► Experimental curves analyzed by multi-oscillatory model of local field. ► This method substantially improves quality of analysis of spectroscopic data for a broad class of crystals.Infrared absorption of (NH4)3WO3F3 compound has been studied. Profile of asymmetric band in 600–1000 cm−1 range associated with polar W–O vibrations of WO 3 F 3 3 - ions is explicable on the basis of multi-oscillatory dynamics with account of damping. Complex profile with Evans holes proves that internal modes of WO 3 F 3 3 - anions in the fluorine–oxygen octahedron interact due to the effects of the local field.