Coherent multidimensional vibrational spectroscopy of biomolecules: concepts, simulations, and challenges.
Coherent multidimensional vibrational spectroscopy of biomolecules: concepts, simulations, and challenges.
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DOI：
10.1002/anie.200802644
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发表时间：
2009
影响因子：
16.6
通讯作者：
Mukamel, Shaul
中科院分区：
文献类型：
--
作者：
Zhuang, Wei;Hayashi, Tomoyuki;Mukamel, Shaul
复杂分子对飞秒红外脉冲序列的响应为它们的结构、动力学和波动环境提供了一个独特的窗口，正如投影到振动自由度中一样。本文综述了这类新型二维红外（2H）多维核磁共振类似物的基本原理。微扰的方法计算耦合本地化的生色团的非线性光学响应的介绍和应用到蛋白质，液态水，膜脂，和淀粉样蛋白原纤维的酰胺主链的转变。信号进行了分析，使用经典的MD模拟结合一个有效的波动哈密顿耦合本地化的非谐振动，其依赖于当地的静电环境参数化从头算映射。几个模拟协议。包括高斯涨落的累积展开（CGF）、准粒子散射方法（NEE）、随机刘维尔方程（SLE）和直接数值传播。这些都是实现在一个代码SPECTRON接口与标准的电子结构和分子机制MD代码。手性诱导的技术，显着提高分辨率的证明。签名的构象和氢键的波动，蛋白质折叠，和化学交换过程进行了讨论。
The response of complex molecules to sequences of femtosecond infrared pulses provides a unique window into their structure, dynamics and fluctuating environments, as projected into the vibrational degrees of freedom. In this review we survey the basic principles of these novel two dimensional infrared (2DIR) analogues of multidimensional NMR. The perturbative approach for computing the nonlinear optical response of coupled localized chromophores is introduced and applied to the amide backbone transitions of protein, liquid water, membrane lipids, and amyloid fibrils. The signals are analyzed using classical MD simulations combined with an effective fluctuating Hamiltonian for coupled localized anharmonic vibrations whose dependence on the local electrostatic environment is parameterized by an ab initio map. Several simulation protocols. Including the Cumulant expansion of Gaussian Fluctuation (CGF), a quasiparticle scattering approach (NEE), the Stochastic Liouville Equations (SLE), and Direct Numerical Propagation are surveyed. These are implemented in a code SPECTRON that interfaces with standard electronic structure and molecular mechanisms MD codes. Chirality-induced techniques which dramatically enhance the resolution are demonstrated. Signatures of conformational and hydrogen bonding fluctuations, protein folding, and chemical exchange processes are discussed.
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影响因子：
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