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1.
J Phys Chem B ; 123(31): 6651-6663, 2019 Aug 08.
Article in English | MEDLINE | ID: mdl-31074985

ABSTRACT

Lithium ion battery (LIB) technology is undoubtedly indispensable to modern life. However, despite enormous and extended effort to improve LIB performance, our understanding of the underlying principles and mechanisms of lithium ion transport in nonaqueous LIB electrolytes remained limited until recently. There is a particular lack of knowledge of the microscopic solvation structures and fluctuation dynamics around charge carriers in real electrolytes. Typical electrolytes found in commercially available LIBs consist of lithium salts and mixed carbonate solvents, with the latter playing an essential role in promoting lithium ion transport and forming an electrically stable solid electrolyte interphase. Although a number of linear spectroscopic studies of LIB electrolytes aiming at understanding the complex nature of lithium ion solvation processes have been reported, the notion that each lithium ion is strongly solvated by carbonate molecules to form a long-lasting solvation sheath structure has remained the subject of intense debate. Here, we present the results of FTIR, fs IR pump-probe, two-dimensional IR spectroscopy, and molecular dynamics simulations reported by us and others and discuss the possible interplay of picosecond solvation dynamics and macroscopic ion transport processes within the framework of the fluctuation-dissipation relationship. Further, by measuring the time-dependent fluctuations and spectral diffusions of carbonate carbonyl stretch modes that act as excellent infrared probes for the local electrostatic environment, we show that lithium cations are not only solvated by carbonate molecules but also interact with counteranions at equilibrium depending on solvent composition. Molecular dynamics simulations support the notion that rapid chemical exchanges between carbonate solvent molecules in the first and outer solvation shells are critical for describing mobile lithium ion transport phenomena. We thus anticipate that time-resolved coherent multidimensional vibrational spectroscopy is capable of providing decisive evidence on the ultrafast solvent dynamics of various electrolytes, which is potentially helpful for designing improved and more efficient LIB electrolytes in the future.

2.
Ann Plast Surg ; 81(5): 537-543, 2018 11.
Article in English | MEDLINE | ID: mdl-29994878

ABSTRACT

We aimed to inspect bowstringing after percutaneous and open release of the A1 pulley for trigger digits and its influence on hand function. Sixty-two patients with a resistant trigger digit were randomized to undergo either open release or percutaneous release of the A1 pulley. We quantified bowstringing of the digit using ultrasonography preoperatively and at 12 and 24 weeks after surgery. Pain on a visual analog scale; Disabilities of the Arm, Shoulder, and Hand questionnaire; pinch power; and grip strength were assessed. Bowstringing was significantly increased at 12 weeks after surgery in both groups, and the mean value of the open release group was significantly greater than that of the percutaneous group (2.30 ± 0.58 mm vs 1.46 ± 0.51 mm, respectively; P = 0.035). However, the bowstringing was decreased at 24 weeks without showing significant difference between the 2 groups. The clinical outcomes of each cohort improved significantly, with no difference between the groups at final follow-up. No association was found between bowstringing and any clinical outcome measure. Bowstringing occurred by A1 pulley release with either the percutaneous or open technique does not affect clinical hand function in patients with trigger fingers.


Subject(s)
Orthopedic Procedures/methods , Trigger Finger Disorder/surgery , Adult , Aged , Disability Evaluation , Female , Hand Strength , Humans , Male , Middle Aged , Pain Measurement , Prospective Studies , Trigger Finger Disorder/diagnostic imaging , Ultrasonography
3.
Foot Ankle Surg ; 23(4): 243-249, 2017 Dec.
Article in English | MEDLINE | ID: mdl-29202982

ABSTRACT

BACKGROUND: To compare the outcomes of fixation methods for osteosynthesis of a type II symptomatic accessory navicular between screw and tension band wiring. METHODS: Forty-four patients (mean age, 29.2 years; range, 13-54 years; 21 males and 23 females) who had undergone operative treatment after failed conservative treatment were chosen for the study between 2007 and 2014. The patients were divided into two groups by the method of osteosynthesis: group 1 (screw) and group 2 (tension band wiring). Pre and postoperative evaluations were performed, using the midfoot scale from the American Orthopaedic Foot and Ankle Society (AOFAS), a visual analog scale, time to return to social activities, and plain radiography. RESULTS: The AOFAS midfoot and visual analog scale scores of both groups were improved at the last postoperative follow-up. The time to return to social activities was 12.3 weeks in the screw group and 11.9 weeks in the tension band wiring group (p=0.394). A broken screw was observed in one case in the screw group and a broken k-wire was detected in two cases in the tension band wiring group. Nonunion was observed in two cases in each group. CONCLUSION: The tension band wiring technique could be another treatment choice of osteosynthesis for fixation of the accessory navicular bone. LEVEL OF EVIDENCE: Level III, Retrospective Case Control Study.


Subject(s)
Foot Diseases/surgery , Fracture Fixation, Internal/methods , Tarsal Bones/abnormalities , Adolescent , Adult , Bone Screws , Bone Wires , Case-Control Studies , Child , Female , Foot Diseases/diagnostic imaging , Humans , Male , Middle Aged , Retrospective Studies , Tarsal Bones/diagnostic imaging , Tarsal Bones/surgery , Treatment Outcome , Young Adult
4.
Article in English | MEDLINE | ID: mdl-28918319

ABSTRACT

Coffee, a complex mixture of more than 800 volatile compounds, is one of the most valuable commodity in the world, whereas caffeine and chlorogenic acids (CGAs) are the most common compounds. CGAs are mainly composed of caffeoylquinic acids (CQAs), dicaffeoylquinic acids (diCQAs), and feruloylquinic acids (FQAs). The major CGAs in coffee are neochlorogenic acid (3-CQA), cryptochlorogenic acid (4-CQA), and chlorogenic acid (5-CQA). Many studies have shown that it is possible to separate the isomers of FQAs by high-performance liquid chromatography (HPLC). However, some authors have shown that it is not possible to separate 4-feruloylquinic acid (4-FQA) and 5-feruloylquinic acid (5-FQA) by HPLC. Therefore, the present study was designated to investigate the chromatographic problems in the determination of CGAs (seven isomers) and caffeine using HPLC-DAD. The values of determination coefficient (R2) calculated from external-standard calibration curves were >0.998. The recovery rates conducted at 3 spiking levels ranged from 99.4% to 106.5% for the CGAs and from 98.8% to 107.1% for the caffeine. The precision values (expressed as relative standard deviations (RSDs)) were <7% and <3% for intra and interday variability, respectively. The tested procedure proved to be robust. The seven CGAs isomers except 4-FQA and 5-FQA were well distinguished and all gave good peak shapes. We have found that 4-FQA and 5-FQA could not be separated using HPLC. The method was extended to investigate the effects of different brewing conditions such as the roasting degree of green coffee bean, coffee-ground size, and numbers of boiling-water pours, on the concentration of CGAs and caffeine in homemade brewed coffee, using nine green coffee bean samples of different origins. It was reported that medium-roasted, fine-ground coffees brewed using three pours of boiling water were the healthiest coffee with fluent CGAs.


Subject(s)
Caffeine/analysis , Chlorogenic Acid/analysis , Coffee/chemistry , Chromatography, High Pressure Liquid/methods , Limit of Detection , Linear Models , Particle Size , Reproducibility of Results , Temperature
5.
J Hand Surg Am ; 41(5): 615-23, 2016 May.
Article in English | MEDLINE | ID: mdl-27039349

ABSTRACT

PURPOSE: The aim of this study was to compare the results of arthroscopic peripheral repair (AR) and arthroscopic debridement (AD) for the treatment of chronic unstable triangular fibrocartilage complex (TFCC) tears in ulnar-positive patients undergoing ulnar-shortening osteotomy (USO). METHODS: A total of 31 patients who underwent arthroscopic treatments combined with USO for unstable TFCC tears and were followed-up at a minimum of 24 months were included in this retrospective cohort study. Fifteen patients were treated with AR, and 16 patients were treated with AD while at the same time undergoing a USO. Outcome measures included wrist range of motion, grip strength, Disabilities of the Arm, Shoulder, and Hand (DASH) and Patient-Rated Wrist Evaluation (PRWE) scores, and overall outcomes according to the modified Mayo wrist scoring system. In addition, a stress test to assess distal radioulnar joint (DRUJ) stability was performed before and after surgery to compare the 2 cohorts. RESULTS: Both respective cohorts showed significant improvements in grip strength and subjective scores at the final follow-up. Grip strength, DASH, and PRWE scores were better in the AR group than in the AD group. The recovery rate from DRUJ instability observed during the preoperative examination was superior in the AR group. CONCLUSIONS: Both AD and AR of the TFCC combined with USO are reliable procedures with satisfactory clinical outcomes for unstable TFCC tears in ulnar-positive patients. However, AR of the TFCC is suggested if DRUJ stability is concomitantly compromised. TYPE OF STUDY/LEVEL OF EVIDENCE: Therapeutic IV.


Subject(s)
Arthroscopy , Debridement , Joint Instability/surgery , Osteotomy , Triangular Fibrocartilage/injuries , Wrist Joint , Adult , Female , Hand Strength , Humans , Male , Middle Aged , Range of Motion, Articular , Retrospective Studies , Treatment Outcome , Ulna/surgery , Young Adult
6.
J Air Waste Manag Assoc ; 62(9): 1085-92, 2012 Sep.
Article in English | MEDLINE | ID: mdl-23019822

ABSTRACT

UNLABELLED: TiO2-supported manganese oxide catalysts formed using different calcination temperatures were prepared by using the wet-impregnation method and were investigated for their activity in the low-temperature selective catalytic reduction (SCR) of NO by NH3 with respect to the Mn valence and lattice oxygen behavior. The surface and bulk properties of these catalysts were examined using Brunauer-Emmett-Teller (BET) surface area, X-ray diffraction (XRD), temperature-programmed reduction (TPR), and temperature-programmed desorption (TPD). Catalysts prepared using lower calcination temperatures, which contained Mn4+ displayed high SCR activity at low temperatures and possessed several acid sites and active oxygen. The TPD analysis determined that the Brönsted and Lewis acid sites in the Mn/TiO2 catalysts were important for the low-temperature SCR at 80-160 and 200-350 degrees C, respectively. In addition, the available lattice oxygen was important for attaining high NO to NO2 oxidation at low temperatures. IMPLICATIONS: Recently, various Mn catalysts have been evaluated as SCR catalysts. However, there have been no studies on the relationship of adsorption and desorption properties and behavior of lattice oxygen according to the valence state for manganese oxides (MnO(x)). Therefore, in this study, the catalysts were prepared by the wet-impregnation method at different calcination temperatures in order to show the difference of manganese oxidation state. These catalysts were then characterized using various physicochemical techniques, including BET, XRD, TPR, and TPD, to understand the structure, oxidation state, redox properties, and adsorption and desorption properties of the Mn/TiO2 catalysts.


Subject(s)
Air Pollution/prevention & control , Ammonia/chemistry , Manganese Compounds/chemistry , Nitric Oxide/chemistry , Oxides/chemistry , Titanium/chemistry , Air Pollutants/chemistry , Catalysis , Oxidation-Reduction , Temperature
7.
J Phys Chem B ; 116(17): 5097-110, 2012 May 03.
Article in English | MEDLINE | ID: mdl-22512849

ABSTRACT

4-Azidoproline (Azp) can tune the stability of the polyproline II (P(II)) conformation in collagen. The azido group in the 4R and 4S configurations stabilizes and destabilizes the P(II) conformation, respectively. To obtain insights into the dependence of the conformational stability on the azido configuration, we carried out Fourier transform (FT) IR experiments with four 4-azidoproline derivatives, Ac-(4R/S)-Azp-(NH/O)Me. We found that the amide I and azido IR spectra are different depending on the azido configuration and C-terminal structure. The origin of such spectral differences between 4R and 4S configurations and between C-terminal methylamide and ester ends was elucidated by quantum chemistry calculations in combination with (1)H NMR and time- and frequency-resolved IR pump-probe spectroscopy. We found that the azido configurations and C-terminal structures affect intramolecular interactions, which are responsible for the ensuing conformational and thereby IR spectral differences. Consequently, 4-azidoproline conformations modulated by azido configurations can be probed by IR spectroscopy. These findings suggest that 4-azidoproline can be both a structure-control and -probing element, which enables the infrared tracking of proline roles in protein structure, function, and dynamics.


Subject(s)
Azides/chemistry , Proline/analogs & derivatives , Amides/chemistry , Molecular Conformation , Proline/chemistry , Quantum Theory , Spectroscopy, Fourier Transform Infrared , Stereoisomerism
8.
J Adv Nurs ; 68(12): 2646-53, 2012 Dec.
Article in English | MEDLINE | ID: mdl-22384945

ABSTRACT

AIM: To report a correlational study of the relation of body mass index to children's perceptions of physical appearance and global self-worth and depression, as mediated by their perceptions of parental teasing. BACKGROUND: The relation between depression and self-perception in children with obesity has been reported. Recently, parental factors were found to be related to childhood obesity. Little is known about the effects of perceived parental teasing on depression and self-perception in children. DESIGN: A descriptive correlational research design was used. METHODS: Data were collected from 455 children in the fifth and sixth grades in four provinces of South Korea using self-report questionnaires for measuring self-perception of physical appearance and global self-worth, depression and perceived parental teasing between October-December in 2009. The children's weight and height information from school health records was used. Multiple regression analysis and the Sobel test were used to identify the mediating effect of perceived parental teasing. RESULTS: Among the children, 20% were overweight or obese. Although children with obesity did not differ in the level of depression from their normal weight counterparts, they demonstrated lower perceived physical appearance and higher perceived parental teasing. The mediating effects of perceived parental teasing were found for the relations between body mass index and self-perception of physical appearance and global self-worth, and body mass index and depression, respectively. CONCLUSION: Obese children at risk of parental teasing should be identified to prevent their psychological problems. A well-designed intervention study is necessary to examine the effects of psycho-emotional interventions for obese children.


Subject(s)
Body Image , Depression/etiology , Overweight/psychology , Parent-Child Relations , Self Concept , Adaptation, Psychological , Body Mass Index , Child , Cross-Sectional Studies , Female , Humans , Male , Multivariate Analysis , Obesity/psychology , Republic of Korea
9.
J Air Waste Manag Assoc ; 61(5): 552-8, 2011 May.
Article in English | MEDLINE | ID: mdl-21608495

ABSTRACT

This study investigated the effect of adding vanadium (V) to natural manganese oxide (NMO) in ammonia (NH3) selective catalytic reduction (SCR). The addition of V to NMO decreased the catalytic activity at low temperatures by blocking the active site. However, the enhancement of catalytic activity was achieved by controlling NH3 oxidation at high temperatures. From the NH3 temperature programmed desorption and oxygen on/off test, it was confirmed that the amount of Lewis acid site and active lattice oxygen of the catalyst affects the catalytic performance at low temperature.


Subject(s)
Ammonia/chemistry , Catalysis , Industrial Waste/prevention & control , Manganese Compounds/chemistry , Oxides/chemistry , Vanadium/chemistry , Air Pollution/prevention & control , Humans , Inhalation Exposure/prevention & control , Nitrogen Dioxide/analysis , Nitrogen Dioxide/toxicity , Oxidation-Reduction , Photoelectron Spectroscopy , Reducing Agents , Temperature
10.
J Chem Phys ; 134(6): 064506, 2011 Feb 14.
Article in English | MEDLINE | ID: mdl-21322704

ABSTRACT

Ultrafast two-dimensional infrared (2DIR) spectroscopy has been proven to be an exceptionally useful method to study chemical exchange processes between different vibrational chromophores under thermal equilibria. Here, we present experimental results on the thermal equilibrium ion pairing dynamics of Li(+) and SCN(-) ions in N,N-dimethylformamide. Li(+) and SCN(-) ions can form a contact ion pair (CIP). Varying the relative concentration of Li(+) in solution, we could control the equilibrium CIP and free SCN(-) concentrations. Since the CN stretch frequency of Li-SCN CIP is blue-shifted by about 16 cm(-1) from that of free SCN(-) ion, the CN stretch IR spectrum is a doublet. The temperature-dependent IR absorption spectra reveal that the CIP formation is an endothermic (0.57 kJ∕mol) process and the CIP state has larger entropy by 3.12 J∕(K mol) than the free ion states. Since the two ionic configurations are spectrally distinguishable, this salt solution is ideally suited for nonlinear IR spectroscopic investigations to study ion pair association and dissociation dynamics. Using polarization-controlled IR pump-probe methods, we first measured the lifetimes and orientational relaxation times of these two forms of ionic configurations. The vibrational population relaxation times of both the free ion and CIP are about 32 ps. However, the orientational relaxation time of the CIP, which is ∼47 ps, is significantly longer than that of the free SCN(-), which is ∼7.7 ps. This clearly indicates that the effective moment of inertia of the CIP is much larger than that of the free SCN(-). Then, using chemical exchange 2DIR spectroscopy and analyzing the diagonal peak and cross-peak amplitude changes with increasing the waiting time, we determined the contact ion pair association and dissociation time constants that are found to be 165 and 190 ps, respectively. The results presented and discussed in this paper are believed to be important, not only because the ion-pairing dynamics is one of the most fundamental physical chemistry problems but also because such molecular ion-ion interactions are of critical importance in understanding Hofmeister effects on protein stability.


Subject(s)
Dimethylformamide/chemistry , Lithium/chemistry , Thermodynamics , Thiocyanates/chemistry , Solutions , Spectrophotometry, Infrared
11.
J Phys Chem B ; 115(18): 5456-64, 2011 May 12.
Article in English | MEDLINE | ID: mdl-21189024

ABSTRACT

Two-dimensional (2D) optical spectroscopy based on stimulated photon echo geometry requires multiple ultrashort pulses of which spatiotemporal properties and optical phases can be precisely controlled. Also, it is possible to change the incident beam polarization directions defined in a laboratory frame. Here, we introduce the polarization-angle-scanning (PAS) 2D spectroscopy and show that the diagonal and cross-peak amplitudes in the 2D spectrum can be arbitrarily modulated by spatially controlling the beam polarization directions. For a coupled anharmonic oscillator system, we specifically demonstrate that either diagonal or cross-peaks in the measured 2DIR spectra can be selectively eliminated and show that such polarization angles provide direct information on the relative angles between coupled transition dipoles and thereby on intricate details of molecular structures. We thus anticipate that the present PAS 2D optical spectroscopy can be a useful experimental method enabling us to probe structural evolutions of nonequilibrium state molecules by monitoring the time-dependent changes of the relative transition dipole directions.

12.
Chemphyschem ; 11(17): 3632-7, 2010 Dec 03.
Article in English | MEDLINE | ID: mdl-21069654

ABSTRACT

Chemical exchange two-dimensional infrared (2DIR) spectroscopy is applied to investigate ion pairing dynamics occurring on picosecond timescales. SeCN(-) ion is used as a vibrational probe. The SeCN(-) ion dissolved in N,N-dimethyl formamide (DMF) has a sufficiently long vibrational lifetime and can form a contact ion pair with Li(+) ion in DMF. The CN stretch frequency of the contact ion pair is significantly blue-shifted from that of free SeCN(-) so the free SeCN(-) ion can be spectrally distinct from the contact ion pair in DMF. Therefore, we were able to directly monitor the ion pairing dynamics of Li(+) and SeCN(-) in real time by using ultrafast 2DIR spectroscopy. As a result, we have determined the dissociation time constant of the LiSeCN contact ion pair to be 420±40 ps.


Subject(s)
Cyanides/chemistry , Ions/chemistry , Lithium/chemistry , Spectrophotometry, Infrared/methods , Dimethylformamide , Selenium Compounds/chemistry
13.
J Phys Chem A ; 114(8): 2757-67, 2010 Mar 04.
Article in English | MEDLINE | ID: mdl-20141151

ABSTRACT

Aromatic compounds with electron-donating or -accepting substituents exhibit interesting resonance effects on a variety of chemical reactivities and optical properties. To understand such effects and the possible relationship between vibrational energy dissipation pathways and resonance structures of aromatic compounds, we studied ortho-, meta-, and para-substituted cyanophenols and their anionic forms in methanol by using time- and frequency-resolved pump-probe and two-dimensional IR spectroscopy, where the nitrile group acts as an IR probe. From the measured transient spectra and singular-value decomposition analyses, we found that there is a combination band whose frequency is very close to that of the nitrile stretch mode. Due to the difference in the lifetimes of these two mode excited states, the transient pump-probe spectra commonly show notable blue-shifting behaviors in time. Comparing the vibrational lifetimes of neutral cyanophenols and cyanophenoxide anions in methanol and carrying out quantum mechanical/molecular mechanical molecular dynamics simulations to study hydrogen-bonding dynamics, we found that the vibrational energy of the nitrile stretch mode initially relaxes to intramolecular degrees of freedom instead of solvent modes. Also, the vibrational anharmonic frequency shifts, intrinsic lifetimes, and bandwidths of the nitrile stretch mode and the combination mode in these molecular systems are fully characterized, and their relationships with resonance structures are discussed. It is believed that the present work sheds light on the intrinsic vibrational relaxation process of the nitrile stretch mode in cyanophenols, even in the case when their IR spectra are congested by the spectrally overlapping combination bands, and the resonance effects of aromatic compounds on vibrational dynamics and relaxation processes.

14.
J Chem Phys ; 130(20): 204509, 2009 May 28.
Article in English | MEDLINE | ID: mdl-19485459

ABSTRACT

By means of integrated and dispersed IR photon echo measurement methods, the vibrational dynamics of C-N stretch modes in 4-cyanophenol and 4-cyanophenoxide in methanol is investigated. The vibrational frequency-frequency correlation function (FFCF) is retrieved from the integrated photon echo signals by assuming that the FFCF is described by two exponential functions with about 400 fs and a few picosecond components. The excited state lifetimes of the C-N stretch modes of neutral and anionic 4-cyanophenols are 1.45 and 0.91 ps, respectively, and the overtone anharmonic frequency shifts are 25 and 28 cm(-1). At short waiting times, a notable underdamped oscillation, which is attributed to a low-frequency intramolecular vibration coupled to the CN stretch, in the integrated and dispersed vibrational echo as well as transient grating signals was observed. The spectral bandwidths of IR absorption and dispersed vibrational echo spectra of the 4-cyanophenoxide are significantly larger than those of its neutral form, indicating that the strong interaction between phenoxide and methanol causes large frequency fluctuation and rapid population relaxation. The resonance effects in a paradisubstituted aromatic compound would be of interest in understanding the conjugation effects and their influences on chemical reactivity of various aromatic compounds in organic solvents.


Subject(s)
Methanol/chemistry , Nitriles/chemistry , Phenols/chemistry , Photons , Vibration , DNA/chemistry , Infrared Rays , Light Signal Transduction , Models, Chemical , Nonlinear Dynamics , Photochemical Processes , Spectrophotometry, Infrared
15.
Stud Health Technol Inform ; 122: 499-502, 2006.
Article in English | MEDLINE | ID: mdl-17102307

ABSTRACT

This study was designed to analyze the time for direct and indirect nursing activity to evaluate the workload of nurses using a full Electronic Medical Record (EMR) system on practice. The result is that the mean time for nursing activity per nurse was 499.56 minutes, the mean time for direct nursing activity per nurse was 251.1 minutes (50.3%), and the mean time for indirect nursing activity per nurse was 248.42 minutes(49.7%). The time for direct nursing activity was more than the time for indirect nursing activity. There was a significant difference in the time for nursing activity according to workplace (p < 0.00*), but no difference according to nursing career. Regarding 3 duty-shifts, the time for direct nursing activity was highest in the evening shift and the time for indirect nursing activity was highest in the night shift.


Subject(s)
Medical Records Systems, Computerized , Nursing Care , Task Performance and Analysis , Data Collection , Humans , Korea , Nursing Staff, Hospital , Time Factors , Workload
16.
J Chem Phys ; 125(11): 114508, 2006 Sep 21.
Article in English | MEDLINE | ID: mdl-16999491

ABSTRACT

Carrying out density functional theory calculations of four DNA bases, base derivatives, Watson-Crick (WC) base pairs, and multiple-layer base pair stacks, we studied vibrational dynamics of delocalized modes with frequency ranging from 1400 to 1800 cm(-1). These modes have been found to be highly sensitive to structure fluctuation and base pair conformation of DNA. By identifying eight fundamental basis modes, it is shown that the normal modes of base pairs and multilayer base pair stacks can be described by linear combinations of these vibrational basis modes. By using the Hessian matrix reconstruction method, vibrational coupling constants between the basis modes are determined for WC base pairs and multilayer systems and are found to be most strongly affected by the hydrogen bonding interaction between bases. It is also found that the propeller twist and buckle motions do not strongly affect vibrational couplings and basis mode frequencies. Numerically simulated IR spectra of guanine-cytosine and adenine-thymine bases pairs as well as of multilayer base pair stacks are presented and described in terms of coupled basis modes. It turns out that, due to the small interlayer base-base vibrational interactions, the IR absorption spectrum of multilayer base pair system does not strongly depend on the number of base pairs.


Subject(s)
Base Pairing , Computer Simulation , DNA/chemistry , Nucleic Acid Conformation , Nucleotides/chemistry , Vibration , Models, Chemical
17.
J Chem Phys ; 125(11): 114510, 2006 Sep 21.
Article in English | MEDLINE | ID: mdl-16999493

ABSTRACT

A theoretical description of the vibrational excitons in DNA is presented by using the vibrational basis mode theory developed in Papers I and II. The parameters obtained from the density functional theory calculations, such as vibrational coupling constants and basis mode frequencies, are used to numerically simulate two-dimensional (2D) IR spectra of dG(n):dC(n) and dA(n):dT(n) double helices with n varying from 1 to 10. From the molecular dynamics simulations of dG(5)C(5) and dA(5)T(5) double helices in D(2)O solution, it is found that the thermally driven internal motions of these systems in an aqueous solution do not induce strong fluctuations of basis mode frequencies nor vibrational couplings. In order to construct the two-exciton Hamiltonian, the vibrational anharmonicities of eight basis modes are obtained by carrying out B3LYP6-31G(*) calculations for the nine basis modes. The simulated 2D IR spectra of dG(n):dC(n) double helix in D(2)O solution are directly compared with closely related experimental results. The 2D IR spectra of dG(n):dC(n) and dA(n):dT(n) are found to be weakly dependent on the number of base pairs. The present work demonstrates that the computational procedure combining quantum chemistry calculation and molecular dynamics simulation methods can be of use to predict 2D IR spectra of nucleic acids in solutions.


Subject(s)
Computer Simulation , DNA/chemistry , Nucleic Acid Conformation , Nucleotides/chemistry , Vibration , Water/chemistry , Base Pairing , Models, Chemical
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