. Author manuscript; available in PMC: 2011 Oct 28.

Published in final edited form as: J Phys Chem B. 2010 Oct 28;114(42):13536–13544. doi: 10.1021/jp106406p

Table 4.

Comparison between measured and simulated frequency for six observations in RNase using different MD sampling strategies. Simulated shifts are calculated relative to the value for EtSCN, m-tolunitrile or p-tolunitrile in n-hexane as described in the text. The dielectric used in calculating the field at the nitrile was ε = 2. Results from either 3 ns of conventional MD sampling or 3 ns of Replica Exchange MD (REMD) sampling are shown.

		Experiment		MD		REMD
RNase- variant	pH	peak [cm⁻¹]	FWHM [cm⁻¹]	peak [cm⁻¹]	FWHM^b [cm⁻¹]	peak [cm⁻¹]	FWHM^b [cm⁻¹]	Null shift^c [cm⁻¹]
SCN	4.5	2154.4	9.0	2154.8	4.5	2155.3	5.4	2162.0
	8.0	2156.2	10	2157.5	4.9	2157.5	6.3	2162.0
pCN	4.5	2231.2	5.9	2234.4	3.1	2233.4	4.2	2233.2
	8.0	2231.5	5.7	2232.5	2.8	2232.7	3.1	2233.2
mCN	4.5	2233.9	10	2230.8^a	7.8 ^a	2232.0^a	7.8 ^a	2233.8
α only				2234.4	8.2	2233.4	8.9
β only				2230.3	5.6	2231.5	6.1
	8.0	2233.4	10	2232.5^a	6.6 ^a	2232.9^a	7.3 ^a
α only				2233.7	8.0	2233.2	8.5
β only				2232.2	4.9	2232.9	5.6
avg. error				0.3		0.5		2.9
RMS error				2.0		1.5		4.1

Calculated from a concatenated trajectory from both α and β conformers.

FWHM approximated as for a Gaussian distribution as $2 \sqrt{2 \ln 2} σ$ where σ is the variance of the distribution of frequencies.

The null shift equals the reference frequency used and provides a comparison of how well the simulation does relative to no electrostatic perturbation.